Cinque Terre

Hard to predict the crowds. Hopefully when all of the day trippers leave it will be much slower at night.
There really is no right answer so you have to look into each and find a personal reason why 1 appeals to you most.
They are small enough and close enough to each other that you can see them all regardless of which 1 you choose as a base.

Early September will be crowded during the day, main issue is likely finding tables for lunch, getting on trains and ferries not hiking though.

Also, make sure you are aware of the most up to date trail status, so many tourist show up quite shocked that two of the main trails are closed, have been for years and likely will be for years.

For me Manarola or Vernazza were best as I feel they are the most picturesque and offer the postcard views you see when you think of or google the Cinque Terre.

Monterosso offers the most options of places to stay and really the only town with true hotels. It looks like a Riviera beach town. It is much larger, has the only nice true beach and many more restuarants and bars. If you like nightlife, you will likely find all 4 of the other towns quite sleepy. Has an old town and a new town and rail wise offers some additional connections other towns may not have as it is a more main stop. It is the only one that car parking is commonly an option where you stay. Trail to Vernazza from Monterosso is open and a must hike if you like hiking. Will all that going for it, many choose it as a base yet it was low on my list because it lacks the postcard view and stacked colored houses I prefer to see each morning/evening from the town I base myself in.
Manarola will be less crowed than Vernazza. Both are very picturesque but Vernazza I think has more to do, more nightlife and of the 4 main trails which 2 are open start or end in Vernazza.
Main drawback to Vernazza is the crowds.
Main drawback to Manarola is both of the major trails are closed that start or end in Manarola.
Yes there are countless other trails which can and do link all of the towns but by most accounts these are more serious hiking trails and often take longer to walk than many tourists will want.
Manarola, Monterosso and Vernazza pricing is similar for places to spend the night with Monterosso likely to have more to select from though you are late to be booking now so may find all 3 towns quite limited.
Riomaggiore I cannot say much about, but to me seems the value option, as I found more places available there and cheaper prices for similar apartments/B&B's in that town. It has a picturesque view as well with the stacked colored houses and also a fair number of bars and restaurants. For some reason it never appealed enough for me to look into it more but the marina is one of the very best places to see the sunset
Corniglia is more for those that want to avoid the crowds and those that want to relax and enjoy the view from above. You are higher up so many places have commanding views. There are some challenges to staying here due to no ferry access and the town is a good stair climb up from the rail station. If you stay by the rail station you get great views and easy access to trails and the train to see the other towns but no good way to get to restaurants, bars, shops. If you stay in town you get access to the town restaurants, bars and shops likely still a great view but then no simple access to the train to reach the other villages.
This will keep away the masses though so you can stay here with least worry about crowds, I would expect the least amount of nightlife in this town though.

In all of the towns it is good to see where the property is on a map and find out how close the rail station is and the harbor is by walking, some places will have quite the climb if they have great views so heavy luggage is a major concern.
If you are too close to the rail station in some towns you could have a noise issue and most likely will have no view to speak of.

Everyone has their favorite of the the 5 towns, mine is Monterosso because of the beach and the restaurants.

but not be too crowded

I'm afraid that that boat has sailed.

In September expect all the towns to be crazy busy, so much so that it isn't the same place that it was 5 or 10 years ago.

Monterosso is the largest, with the most facilities and the most choice.

Don't be surprised if most of your choices are sold out this close to arrival - just 2 and a half months out. Many of the best places will have filled in February or March.

Good luck with your search.... if Ken sees this he may have some suggestions.

The cruise ship crowds and other day-trippers should be gone by dinner time. I might generalize that each town has roughly enough restaurant capacity to match it's hotel capacity. You won't go hungry, but might have to try a couple of places before finding a table, or wait for one. You can also make a dinner reservation by phone or by stopping by the day before or earlier the same day.

Here I am! The first reply provided a good summary of the Cinque Terre towns. I tend to prefer Monterosso as it's the largest of the five and has the greatest number of hotels, restaurants and other tourist amenities. and also the nicest beaches. The restaurants in all the towns are often busy in the evenings but not as hectic as during the mid part of the day. For some reason, Vernazza seems to be more popular than the other towns, and since it's more "compact" the crowds can be a real problem during the day. Monterosso is larger and has both a "new town" and an "old town" so it seems to absorb the crowds better.

As Nigel mentioned, you may find it challenging to find a hotel vacancy at this late date. I normally start booking in February or March for travel in September. Given the larger number of properties, I'd suggest starting your search in Monterosso. Do you have a copy of the RS Italy guidebook? There are hotel listings there for all the towns. If you need other suggestions, post another note here. You could also consider staying in Levanto. It's not officially one of the C.T. towns, but is only about five minutes from Monterosso by train. Levanto also has a great beach.

If you were planning to go "hiking through all the towns" using the popular Sentiero Azzurro trails, note that only two of the four segments are currently open, and that likely won't change anytime soon. You'll have to purchase a Park Pass to hike the two open segments, but those are inexpensive and easily available. There's an extensive network of other trails in that area, but they tend to go higher in the hills so are a more robust hike. The easiest way to travel between the towns is via the frequent local trains, as travel time from one town to another is only about five minutes each. If you want a more scenic view, take the Ferry (weather permitting).

Thank you everyone for the replies and info! It must be my lucky day because I was able to secure a room at Camere Fontana Vecchia in Vernazza. I think we will make that our base for the two nights. I appreciate the help.

jp,

It's great to hear that you have a room booked, as that's often difficult on such short notice. If there are cruise ships in the area, try not to be in Vernazza during the day!!!