9 day itinerary for late September advice

You have chosen very popular islands to visit. All are good. However you have not taken into consideration the time required to make a ferry hop from one Island to another. You should be aware even a short hop is going to take up half a day because of the ferry time tables. So your plan will give you about a day and a half for each island. Your hotels are going to want you to check out at noon at the latest so you are going to spend lots of time at the ferry ports just waiting for a ferry.
Logistics are important when ferry hopping.
Here is something to consider.
I would suggest you get to Naxos. There are excursion boats to Mykonos with a bonus stop at the ancient site at Delos. Return to Naxos in the late afternoon.
You can also take an excursion to boat to Santorini and back to Naxos in the late afternoon.
I would choose to go to Naxos and just stay there for a few days. At least that plan gives you time to relax and enjoy Naxos .. Honestly you need a week in Naxos just to experience some of it.
By the way, itinerary 2 has one less island hop which makes the logistics better than option 1.
Slow down your time is limited do not waste precious time ferry hopping each day.
Here is why Naxos has it all.
https://www.flickr.com/photos/stanbr54/albums/72177720334044112/
https://www.flickr.com/photos/stanbr54/albums/72177720329571437/

If you're going to party with your friend(s), go to Mykonos and stay there. The island is made for that, and practically 365 days a year, 24/7.

https://youtu.be/dMpaksY4sTE

https://youtu.be/wegUM2i5eRI

Obviously, you will need to account for the budget that goes with it. Mykonos is one of the most expensive places in Europe.

Why would you want to waste your time on ferry trips, especially since you are planning to stay on each island for a very short time? As stanbr explained, you shouldn't measure by distance, but rather by ferry schedules and transfer times, which take at least half a day for every move from one island to another.

Santorini isn't necessarily interesting in terms of culture (except for Akrotiri) and partying (although there are quite a few cocktail bars with DJs in Fira). It is primarily for its landscapes and perhaps its wineries.

Naxos is too big an island to suit your plans.

Thank you both for your advice. We are in our mid 30s so we’re not looking to party the whole time hence the only 3 days in Mykonos.

It’s also our first time in Greece hence the selection of two of the most popular islands.

I looked at the ferry schedule and Mykonos to Naxos is only around 35 minutes. I’m curious how the ferry process takes up half a day?

I know Santorini is a romantic destination. Given this is a group of guys who want to explore and do outdoor activities, would we be better off going to Paris or Naxos instead? Is Santorini a must see?

"I looked at the ferry schedule and Mykonos to Naxos is only around 35
minutes. I’m curious how the ferry process takes up half a day?"

You are forgetting a few details:

Do you know that the ports of Mykonos and Santorini are far from the towns?

Do you know how to get to the port and how long it will take?

Do you know how early you need to be at the dock before the ferry departs?

Do you know how long it takes to disembark from the ferry and get to your hotel, and how you will get there?

Depending on the ferry's time, what do you do with your luggage given the usual check-out before 10:00 AM and/or check-in after 2:00 PM?

Example Island-to-Island Travel Timeline (Assuming a 12:00 PM Ferry)

09:30 AM – Hotel Check-out: Leaving your room and managing your luggage (storing it at reception or carrying it).

09:30 AM – 10:00 AM – Transport to the Port: Traveling to the port (the Port of Tourlos in Mykonos is outside the town center).

10:00 AM – 12:00 PM – Arrival and Pre-Boarding: Arriving at the port early, dealing with crowds, waiting in the terminal, and boarding (If the ferry is on time).

12:00 PM – 12:35 PM – Ferry Crossing: The actual 35-minute boat ride from Mykonos to Naxos.

12:35 PM – 01:00 PM – Disembarkation: Waiting in line with hundreds of other passengers and vehicles to exit the ferry.

01:00 PM – 01:30 PM – Transfer to the New Hotel: walking or taxi or transfer from the port to your accommodation.

01:30 PM – Arrival: Reaching your new hotel, waiting for your room to be ready or leaving bags until the 2:00 PM check-in.

Total Time Consumed: Approximately 4.5 hours of logistical transitions for a nominal 35-minute sea crossing.

So, did you know that the ports of Mykonos and Santorini are far from the towns?

Depending on the ferry time, do you know what you'll do with your luggage, given the usual checkout before 10:00 AM and check-in after 2:00 PM?

Create a timeline and see how long it takes you to travel from one island to another.

Thank you so much for that overview. That’s really helpful!

Will Santorini in late September still be crowded with tourists and couples?

Would we have a better first-time Greece experience in Paros or Naxos instead?

My wife and I were in Santorini (Fira) around this time. During the day, the cruise ships come in and the town is very busy. Evenings are much calmer, tho I didn't really see a party vibe. You can take the public bus to/from the ferry port-Fira, it's very easy even if you're not familiar with public transit.

Will Santorini in late September still be crowded with tourists and
couples?

What makes Santorini unique nowadays (apart from its landscapes) is that there are now more questions about crowds than about things to do. That goes to show how much it matters.

September is still in peak season. According to official stats, around 500,000 visitors arrive in September (Santorini's permanent population is 15,000). That is indeed fewer than in July or August, which each receive 700,000 visitors.

Regarding the "timeline" I mentioned earlier, you can indeed use the bus to get to the Santorini port. It is actually just a short trip of barely 20 minutes if you just look at a map and say "it's very close!", but keep in mind that bus departures are synchronized with ferry departures and leave from Fira between 60 and 90 minutes before the ferry departs.
So, it's another good example: for a journey that seems to take barely 20 minutes, you need to allow at least 2h before the ferry's departure time to ensure you reach the Fira bus station on time.

In my opinion, Paros and Naxos are too big for a stay of only 2 or 3 nights, so I don't see how that could be better in your case.

Thank you for your guidance! This is all extremely helpful.
Santorini seems like it still going to be quite crowded. So I’ll rule it out

We’re looking for nightlife and the ability to do activities (cliff diving, atv, or scuba diving)
What island do you recommend we go?
It sounded like Paros has all the above but my info may be wrong.

I am OK if I cannot explore the whole island.

It sounded like Paros has all the above but my info may be wrong.

Paros could actually be your best bet (I've spent about a month there across a few different trips). In that case, skip Mykonos.

As for Naxos, where I've also spent a good amount of time, it doesn't seem like the best fit for what you're looking for. RS forum members here will likely steer you toward the part I find the least interesting—around Chora, the main town, which is better suited for a quiet vacation for retirees or pre-retirees (shops, organized beaches) rather than active, sporty vibes and nightlife. So, skip Naxos too.

On Paros, even though I usually suggest avoiding Naouss, a pretty fishing port turned into the island's "mini Mykonos" (and very touristy), it should actually be the right spot for you if you want some nightlife at prices more reasonable than Mykonos. Note, though, that Naoussa's actual beach is pretty lame.

https://naoussaparos.com/

Parikia, the capital and port, also offers some fun and swimming options, but with a more family-friendly vibe.

As for activities, like on most islands, it's mostly about water sports. On Paros, I know the spots around Golden Beach, the island's largest and most beautiful beach on the east coast facing Naxos. In that area, you'll find tons of water sports clubs and accommodations with a young, laid-back vibe.
I know Louridis Studio, which offers reasonably priced stays, a great atmosphere, a beach bar, and all kinds of activities nearby.
Since I'm not in your shoes, check it out for yourselves, all of this is in the same area (non-exhaustive list):

https://paros-studios.gr/

https://parosdivingcenter.com/

https://parosdivers.com/

https://force7paros.gr/

https://maps.app.goo.gl/ij1n4gjQTS7cgFCB7

There are also a few cool evening bars around to kick back with new friends you meet during your days in the water and on the beach (pretty tempting, right? lol).

Plus, since island-hopping is your thing, you can head over to Antiparos in about 20 minutes on boats leaving from the port of Punda in Paros.

https://antiparos.com/

General info on Paros:

https://imagine.paros.gr/en/

The bus network on Paros is good, but if you want complete freedom of movement rent a car, scooter, or ATV.
Just watch out for the local laws regarding ATV or scooter rentals (especially ATVs, which, when driven by beginners, have caused some serious or even fatal accidents). Greek rules are strict, so make sure to check the required licenses by reviewing the "Terms & Conditions" on the rental sites.

Regarding the Piraeus-Paros route, there are at least 6 ferries daily, with a crossing time of between 2.5 and 4 hours depending on the type of ferry. There is also an airport with flights to and from Athens.

To sum it up, here's my advice: Go to Paros, maybe plan a day trip or a few nights in Antiparos, and then head back to Athens. It'll keep things simple and maximize your time, and I honestly don't see how you could be disappointed!

So, here is a revised itinerary—simple, efficient, and tailored (based on my suggestions). It can be shifted by a day depending on your arrival time in Greece on September 18 and whether you are taking a flight or a ferry.

Day 1 or 2: Athens to Paros (by flight or ferry)

Day 2 or 3 through Day 6 or 7: Paros, with a possible day trip or short stay on Antiparos

Day 7 or 8: Return to Athens

Thank you both for your feedback! It’s really helping shape the itinerary.
My group is struggling to forego Santorini for Paros.
Given your vast experience traveling to the islands, do you feel like we are making a mistake not going to Santorini at all?

Is there anything that would make the trade off easier to swallow? I’d imagine the crowds would be enough to sway the group.

Nobody can make this decision for you. You're grown adults, you know what you're looking for. You asked questions, you got answers. I gave my opinion, others gave theirs. It's up to you to make the choice that seems best to you.

To drive the point home about the Santorini pictures:
Look at the picture-perfect side versus the behind-the-scenes view, taken at the exact same spot.

https://photos.app.goo.gl/4s216cNZUMKxGWi97

https://photos.app.goo.gl/Hta7WeTuUzotZs9F6

Thanks for your feedback JoLui. I am looking for opinions from a few others as the no clear options has risen to the top.

I was in Santorini in early October and it was crowded with cruise ships and tour buses. I stayed 4 full days though and had the flexibility to hike to Oia from Fira on the day there were no cruise ships in the port. Fira's center was crowded every day and Oia was insane even without cruise ships. I couldn't wait to get out of Oia. The hike was the best part because of the views. I was able to visit Akrotiri as well. Santorini was very hot and humid even in October. With your second itinerary, you will have 3 full days in Santorini. The first one doesn't leave it much time.

You only have 1-2 full days in Athens in both itineraries, which isn't sufficient to visit some of the archeological sites as well as enjoy the current city. If you are really interested in both ancient and modern Athens, you should allow at least 3 full days.

I haven't been to Paros yet (will be going this fall), so cannot compare it with Santorini yet.

It is not clear to me if you arriving in Greece on 9/18 and departing on 9/27? If so, those are travel days and you may not be able to do much sightseeing. Furthermore, do you need to account for jetlag as well?

Figure out how many full days you actually have for things your group is interested in and decide how to adjust your itinerary.