Cinque de Terra

I assume you're referring to the Cinque Terre?

"Where to stay" is somewhat subjective, as most of us here have a favourite of the five towns. I much prefer Monterosso, which is the largest and therefore has the greatest number of hotels, restaurants and other amenities (as well as the best beaches). Monterosso consists of an "old town" and a "new town" so tends to absorb crowds better. Vernazza is also very popular with many here, and hopefully some of them will comment on this thread. Vernazza is smaller so doesn't handle the crowds as well and at times it can be very crowded.

Mid-September crowds will likely be high on days when cruise ships are in the area, but other than that the crowds should be moderate during the peak part of the day.

Which of the trails are you planning to hike? If that includes the popular Sentiero Azzurro trails, note that only two of the four segments are currently open (Park pass required to hike those).

At that time of year, I'd suggest getting lodgings booked soon. Once you've decided on which town you'd prefer to stay in, I'm sure the group here can provide some suggestions for hotels or other accommodations. If you'd prefer more of a "standard" hotel that provides breakfast and staff to help if you need anything, Monterosso is the best choice as many of the lodgings in the other towns are just private rooms so you wouldn't get breakfast.

Mid Sept will be very crowded
Cruises seem to be popular in nearby ports at this time which makes the villages overcrowded mid day

I would book a place to stay immediately if you want to stay in 1 of the 5 villages. I am sure most options in vernazza are already fully booked. vernazza does not have many options to begin with
Monterosso may have more options if you want to expand your search

We are going for the first time in early September. Vernazza was highly recommended (RS forums & personal friends). It's my understanding while this town has few lodging options, it resembles the most traditional feel of CT. We have booked a room at FrancaMaria. We had to adjust our dates to get a room (this was well over a month ago..) I suggest you contact them directly (via email fr. their website)- be patient. On travel sites, the rooms were all booked. Consider what's important to you-- close to the train, right in town or are you willing to enjoy a "stroll"-- probably up hill, right? There really aren't that many places but that's where we wanted to be. I'm guessing you can't go wrong at any town but we wanted to be in the harbor and where the action will be (even if it's touristy) so it may be smart to learn a little about the differences between the towns... While it will be late for your plans, I do plan to share our experience at this lodging.

Thank you all for the guidance. Appears we may need to make lodging reservations soon. Regarding which trails we plan to hike.....good question. Will assume as many as our days will allow but certainly looking for suggestions. We've been busy planning for the TMB and need to switch gears and start planning this phase of our trip.

My husband and I stayed in Vernazza at Camere Fontanavecchia. The owner, Annamaria, was a gem, and the room we stayed in was perfect for us. The location was also perfect, as it was just a few minutes' walk up the road from the train station and away from the noise of the harbor (not that the noise is bad, mind you). It also was across the road from a laundromat and an ATM, as well as Il Pirata, a great place for a drink and cannoli (as well as a meal, although we didn't dine there). Camere Fontanavecchia also was the best deal of our trip at 70 euro/night.
And while you're in Vernazza, you must go to Franco's Bar La Torre. You'll need to ask directions for it, but once you clamber up the stony footpath to get there, you'll be amazed at this awesome bar/dining spot perched on the cliffs overlooking the sea. It was definitely a highlight of our trip. (Take a flashlight...you may need it to clamber back down those stone steps after dark.)

"Regarding which trails we plan to hike.....good question. Will assume as many as our days will allow but certainly looking for suggestions."

There's an extensive network of trails in that area in addition to the popular Sentiero Azzurro trails, but many of the others go higher into the hills so are a more robust (but not difficult) hike. Which ones to choose will depend on your hiking ability and how much time you want to spend with that activity. One possibility would be to hike the two open sections of the Sentiero Azzurro (Monterosso - Vernazza and Vernazza - Corniglia). You could stop for lunch in either Vernazza or Corniglia. After that use the higher trails to bypass the two closed sections, ending the hike in Riomaggiore. That will probably take the better part of a day.

The Monterosso to Vernazza segment is the most challenging, as there's a steep climb at the Monterosso end. Once you get up to the level of the trail, it's not difficult although there are some narrow sections. The next segment from Vernazza to Corniglia is also somewhat challenging, but not difficult. Whichever trails you choose, be sure to take lots of water.

The official Park website provides a good map of the trails.....

http://www.parconazionale5terre.it/sentieri-outdoor.php

Cant recommend Monterosso enough. Stay in the old town. It is absolutely gorgeous.