Can't address your three questions directly, but do have a recommendation for a side trip from Mykonos. Take a local boat or tour to Delos. Absolutely, in my opinion, a must see.

What else is on your itinerary? if only that, head to Mykonos sooner, then spend days at the end in Athens before flying out.

What time of year? July and August are very crowded and expensive, My/June not bad, September Ideal, other months start to fade.

1: Where to stay...near Mykonos town the best, but near the port the clubs go all night, so noise can be a problem. The best Beaches are along the South shore, so something from Mykonos town to the South can be Convenient.

2: Nicest beach is a matter of what you want. All have crystal clear water, more small pebbles than sand, water is calm and warm.

- Paradise Beach has a couple clubs, lots of music, decent food, party crowd (well in the afternoon and evening after recovering from the night before) and a mix of clothed, topless, and full nude sunbathers.
- Super Paradise has less of a club vibe, again a mix of clothing options, and a dedicated gay community.
- Psarrou, Platis Gialos, and Elia are all more traditional beaches, lots of services, more family friendly, though still topless would be not unusual, and all have more room than the two above.
Buses go to most beaches, there are also boats that go up and down the coast.

3: If I were heading to Mykonos immediately, I would fly there as part of my incoming flight then ferry back to Athens, Otherwise the ferry is short enough to just take that each way.

I agree with the previous poster, do a tour to Delos.

Thank you for that information We are heading out on September 3 - 14th. Still working o the hotel part of our trip.
Delos is just a day trip not a 5 day stay ?? Choose that over Mykonos? 2 adults traveling so the topless in not a big deal but it is not something I intend on doing so I would probably prefer one that is not totally topless. Although I do enjoy nightlife I would not enjoy lots of noise.

Delos is a small island off Mykonos that is an archaeological site...no hotels or population other than maybe a caretaker. You catch a tour boat from the harbor, you go over spend what time you want, catch the boat back. So you would stay in Mykonos. For a couple, don't worry then about the beaches, nobody will care about your preferred method of sunbathing or have an expectation you "join in" to one of the lesser clothed options (though it can be an experience to remember if you do partake)

September is a nice time to visit Mykonos! Nice weather but less crowded!

So:
1. I would propose staying at the town. It's quite lively and you can take the bus/car to go to the beaches
2. I've heard about Ftelia
3. I would recommend ferries. The view is nice and the trip from Rafina port is quite short (3-4 hours). Check www.ferryhopper.com for the timetables from Piraeus and Rafina

What port do I use to take the ferry from Athens to Mykonos and back? Does it depend on where I am staying?
On our last day we will head back to the airport , is there a port closer to the airport in Athens that I am better off using ?

Has anyone visited the island of Kefalonia? I was told this island has the best beaches and not as expensive as Mykonos.

Mykonos is renowned for its nightlife and not for the beaches. Although there are quite nice ones there, Kefalonia and Zante have
even more amazing beaches.

If you still want to go to Mykonos, I would suggest Rafina port as the ferry trip is shorter by 2hours.

Mykonos has only one port, From Athens, the main port is Piraeus, but as another poster mentioned, Rafina can be handy, especially from the Airport.

I think most people though would caution you though about catching a ferry from Mykonos to catch a flight out of Athens the same day. Ferries are subject to the weather and September can have some strong winds, cancelling ferries. I would save 1 or 2 nights for Athens at the end.

Another thing to pass on...There is a harvest festival at the agricultural museum on the second Sunday in September (this year Sept. 10?) When we went 10 years ago or so it was like a big local picnic with food, wine and music...not sure what it is like now, but worth looking into.

If you are looking for beaches, I'd go to Naxos. You could take a day trip to Mykonos & Delos.

I would fly directly to Naxos upon arriving in Athens, if you can find a flight that works with your schedule. Then fly or ferry back to Athens & have all your Athens time at the end of your trip.

So the plan has changes to go to the island first, then finish off the vacation in Athens. Still trying to decide which island to visit was hoping to go to one that is close to Athens as our flight to Athens is long. but the nicer beaches may not be that close.

where do I make arrangements for the flights from Athens to the Islands?

Either Olympic or Aegean Airlines are good for the Islands. Worth noting that nearly all flights are between Athens and an Island, very few flights between islands, except a few other major cities (Heraklion...Thessoloniki) may have routes to the islands as well.

If you do choose Naxos ( which by the way has better beaches, mountain villages some antiquities and the same architecture as Mykonos but at half the price) Sky Express is also flying to Naxos from Athens this year. This is allowing for more people being able to fly. Its a 45 minute flight.
Naxos Town http://www.flickr.com/photos/stanbr54/sets/72157632094558042/
Trip around Naxos http://www.flickr.com/photos/stanbr54/sets/72157634605629689/

Yes Mykonos very expensive for the hotels as I am doing my research, they are beautiful hotels. Naxos is an option the hotels are less expensive than Mykonos , do you recommend staying in the city center , not much hotels to choose from near the beaches.
Any other island that is worth staying for 6 nights that have nice beaches that I may wnat to look into.

If you choose Naxos we always stay at St George beach Agios Georgios. Its part of Naxos town but only a 10 minute strool into town. You get all the activities of town plus a beach vacation. There are better beaches on the west coast but we love diningin town and don't want the commute .

If you really want a beach holiday and don't car about the town then consider Plaka beach. There is no village but a string of tavernas and hotels strung along a three kilometer sand beach. If you want a village Ag Prokopus and Aggia Anna have beach and village combinations.
St George Beach Hotels Naxos http://www.flickr.com/photos/stanbr54/sets/72157632162394787/
St George Beach Naxos http://www.flickr.com/photos/stanbr54/sets/72157632113170279/
Plaka beach tavernas hotels https://www.flickr.com/photos/stanbr54/sets/72157655106193251
Aggia Anna and Ag Prokipos beach areas https://www.flickr.com/photos/stanbr54/albums/72157656297072028

I second Naxos . . . one of Greece's loveliest islands with a wonderful combination of Old & New World Greece. Spectacular mountain ride, hillside villages, archeological sites, beaches, churches, goats, sheeps . . . everything most people want when they go to a Greek Island if you prefer more culture and tradition than nightlife and partying.

I did a day cruise in October to Delos/Mykonos and loved Delos . . . a world-class archeological site. Mykonos, while visually stunning, was just too crowded and touristy. I assume September could be even worse, even though it's considered off-season.

But to each their own. Everyone has their own idea of a Greek Island. Just do your research to make sure you are making the right choice.

We are not nightlife people, we enjoy good food and music entertainment. Naxos is looking like a good fit, but the flights are very limited from Athens to Naxos. How is the ferry trip?
I am also looking at Kefalonia, the beaches look amazing, again limited flights , either way we are looking at spending a few hrs at the airport in Athens which I was hoping to avoid.

Now that my flight is confirmed for Athens , I cant get a flight from Athens to Naxos, there are only a few and they are before we arrive in Athens. Is that normal or do they add more . We arrive on Sept 3rd at noon time and they only flight is at 17:35 that 5hrs wait at the airport and they have no price listed so I cant even choose that flight, does that mean it has not been scheduled. ? is that what that means. I am stressing as I have not booked the hotel in Naxos due to this.
Any ideas??

Regards
Ester

Ester, do not stress … I”ve found a Naxos solution for you. Promise me, do NOT go to Kefalonia, just based on some beach photos, it’s not what you want. Stick with Naxos/ St. George Beach, that’s your best bet in September, listen to Stanbr and me, we’re in your “category” and have tried dozens of islands and That island and St. G. are the best “fit” for you. As both stanbr & I have found, it's so nice to stay ON a beach, early morning walks, lovely sunset sits, & stroll into town for dinner & its many attractions, no need for car or taxi. Then you can take a frequent bus (20-25 min ride) to the outer beaches, my fave is Plaka.

Here are 2 options for you:

1 - PAROS flilght - Naxos quickie ferry

• On Sept 3, that afternoon flight is Sold Out (that’s why no price). However, there IS a good flight to PAROS, which is right NEXT to NAxos (in fact, standing on the beach, you're staring at Paros, right across the water). There’s a 40-minute flight to PAROS on Sept 3 at 14:15 (2:15pm ), you’re supposed to check in 1 hr ahead. Arrives Paros 2:55 … €86.

• 15 minute Taxi to port town (Parikia) about €5-8. a cute little B & B to stay is Casa Di Roma -- right in the Port town surrounded by a nice garden AND a little pool … Just think! by 3:30, you could be in a swimsuit … check booking. com they had 1 double left @ $49 (free cancellation w. advance notice), so I’d suggest you book NOW. At dinner, walk just NORTH of Pier along the shore a whole row of restaurants facing the sunset. I like Aeolis. PS if u cant get Casa di Roma, Hotel Dina is also nice in Parikia, but no pool.

• Next AM after breakfast, roll your bags to the pier and you have an array of Naxos-bound ferries to choose from, all of which will have seats available to buy just before boarding 10:30 (arr 11) 10:35 (arr 11:15) 11:45 (arr 12:30).

• On arrival, if you’ve alerted your NAXOS hotel, most will meet u at the ferry with car or shuttle-bus. The first week in Sept is a busy time and many of the hotels directly on the beach are full but doing a "dummy booking" on booking.com for a 5-nite stay, I see availabilities at several just off the beach, balconies w. beach sea view etc. Check booking.com for Argo Boutique hotel, Galizia Studios, studios Panos, Diogenes Studios, Aegeon Hotel. For Upmarket choice, See Naxos Resort beach hotel. Only the latter 2 have pools, but who needs them.

2 - HAVEN NEAR AIRPORT - Early AM flight

This Option is Only if you can book the cute St Thomas B & B 10 minutes from Airport, 3 rooms, pool, in an olive grove relax, get a take-away dinner & buffet breakfast, catch 10 AM flight to Naxos Monday… but the Paros option is much more attractive, because you’re on an island immediately,

Note -- I did NOT plan that fancy BIG TYPE subheading ... it's weird what a website format will come up with!

You are a life saver, flight is book and so is Casa di Roma. I should also book the ferry for the following day , do you agree?

No, no ferry reservation. it's a 45 minute trip, the ferries will be large .... 400 - 500 people for the smallest, then for the BLUE STAR, 1200 - 1800 people, In September they'll be half-full. Just buy the morning you go... tic ket offices at pierside.