Cinque Terre - Two nights in September

Trains:
http://www.trenitalia.com/tcom-en

Hikes:
http://www.parconazionale5terre.it/Eindex.php

Ferries:
http://www.navigazionegolfodeipoeti.it/en

etc.
http://www.cinqueterre.it/

If you have not booked overnight accommodations, do it ASAP. Several months ago when I booked a spot, already there were no rooms available in 2 of the Monterosso hotels I wanted to stay in. These are very small towns and the rooms are snapped up very quickly.

Yeah, mid-September there will be limited options.
Look at the options in all 5 towns, don't go into your search limited to just one of the towns since you are booking late.

Corniglia is the only one not served by Ferry, so if you eliminate that one you still have 4 to choose from.

River,

As the others have mentioned it's important to book hotels early in the Cinque Terre, especially as September is somewhat of a "peak" month there.

Given the late date I'd suggest starting your search for accommodations in Monterosso (the most northerly of the five towns). It's the largest and therefore has the greatest number of hotels and other lodgings. If you have the RS Italy guidebook, that has listings for a number of reliable places in Monterosso (and the other towns). For the most part, only Monterosso has "regular" hotels as most of the lodgings in the other towns are just small rooms, and in some cases these don't provide breakfast.

The Ferries are easily accessible from all the towns except Corniglia. Note that Ferries are weather-dependent so if the seas are rough, they won't be operating. It's very easy to get between the towns using the frequent and inexpensive local trains.

You can always check dates on Air bnb, there are always cancellations.

IMO, the rooms on air bnb look much more interesting than the CT hotels.

We stayed in Monterosso and were glad that we did, as we appreciated the access to the beach (just to even read on a beach chair after walking around all day) and having more shops/restaurants around. We stayed at Hotel Colonnina (a reco from the RS book) and really liked it, as did a co-worker that I referred there. The trains between the towns are really easy to use, you just need to check to make sure that train stops at the town you want, as they don't all stop at all of the towns (we always checked potential departure times on arrival). Unfortunately, when we were there, only one of the hiking trails between the towns was open and it was the big/long one, so we didn't do it.

In Vernazza, try:

http://www.elisabettacarro.it/ She will be booked but seems to always find a place with a "cousin".

Hotel Pasquale in Monterosso if thy have space

Hi,
We just got back from 5 nights in Cinque Terre(mid-july) and based in Riomaggiore because it had the closest sea view of all the 5 villages and it is the 1st of the 5 villages with easy location to other destinations. We stayed at Atlantis apartment with Alla Marina, which is a Rick Steves pic. The apartment was large 2bedrom/2 full bath showers( wonderful new hot showers) and bonus was a large up close sea view terrace. Has sofa sleeper so it sleeps 6. The owner, Sandro is wonderful and takes care of all your needs. He even bought us ice cube trays and an extra terrace chair and delivered it the next day. We took the ferry almost everyday because the view of the villages from the water is so beautiful. Ferry office is 5 minutes from B&B. The ferry is slow-moving and cost 9 euro one-way between villages. It runs about every 30-45 minutes and is on time. It does not take credit cards.In fact, a lot of smaller places in Cinque Terre do not take credit cards, so bring euros. Hiking is great and scenic, but many STEEP steps and few hand rails. If you have time do not miss the island of Portovenere(via ferry). It cost 24 euro round trip and takes about 1 1/2hours. It is every bit as pretty as Portofino and larger. And you see all 5 villages of Cinque Terre from the ferry....beautiful! As you can tell, my theme is THE WATER! Hope this helps.

Hello,
If you haven't a car in my opinion the best base is Monterosso. It's the biggest village and also the best communicate by trains and there are more services (accommodations, restaurants etc.).

However, if you need more information here you can find some interesting tips:

https://www.mycinqueterre.com/ (Travel and Tourism website about Cinque Terre)

http://www.parconazionale5terre.it/Eindex.php (The Official website of the National Park of Cinque Terre)

http://www.italianfix.com/what-to-do-cinque-terre/ (Another interesting post with some travel tips about Cinque Terre)

I wish you all the best