kapri,
To begin with, I'd suggest changing the order to Venice > Florence > Cinque Terre > Amalfi Coast, as it's much more efficient and avoids backtracking. I'd also suggest making your visit to the C.T. three nights, as that will allow two full days of touring. You may find after you get there that you wish you had booked more time.
The decision on which town to stay is somewhat of a personal preference and each of us here have our favourites. My preference is most definitely Monterosso as it's the largest of the five and has the greatest number of hotels, restaurants and other tourist amenities, as well as the best beaches. Also, as it's larger and has both an "old town" and "new town", it tends to absorb the crowds better (although it can also be crowded in the afternoons). If you prefer a "regular" hotel with desk staff, elevators (in some cases) and a good breakfast, then Monterosso is a perfect choice. It can also be crowded in the afternoons as I found with this lot in September, which plugged the entrance to the station and were embroiled in a fierce argument. This crowd was German and Austrian bus tours, and not from the cruise ships.
Vernazza seems to be the most popular of the five towns, and seems to be promoted more by travel writers (I won't mention any names). The iconic view of the harbour from the trail seems to be the preferred image on many travel brochures and websites. People planning a visit especially for the first time may focus only on that image and think that's the only place to stay in the C.T. There are four other towns however, and each of them has a unique character.
I've been to Vernazza a number of times, but after a dreadful experience a couple of years ago, I've tended to avoid the place but I will try to get there on my next trip and explore the town more. I made the mistake of travelling from Monterosso to Vernazza one afternoon (about 16:00). When I first ventured onto the platform at the Monterosso station, there were only a few people waiting. That changed quickly however when three cruise ship groups arrived, each with about 60-70 people along with their umbrella-toting guides. The trip to Vernazza only took about seven minutes, but it was strictly SRO, elbow-to-elbow on a hot and stuffy train. When the train arrived in Vernazza, it took me 20 minutes or more to get just from the station platform down to the main street in town. I was stuck in a tunnel for part of that time. By that time I was very much regretting my decision to make that trip. Unfortunately, the boats were close to shutting down for the day, so that wasn't an option. When I finally got down to the street, that was also pretty much elbow-to-elbow and not a pleasant experience. I can't blame the other travellers from wanting to see Vernazza as that's I was also there for, but it was still a most unpleasant experience.
Over the years, I've been fine-tuning ways to minimize the crowding problems in the Cinque Terre, and have found some success with that. For example in the afternoons when the towns are most crowded, I'm either touring in another area OR sitting on the wonderfully comfortable balcony of my hotel far above the madding crowd, with a cool glass of Prosecco (or three). I also try to go for lunch at non-standard times (ie: 14:00) as the restaurants and Bars are usually less crowded at that time. The evenings can also be hectic in the restaurants, but not to the same degree as during the daytime. I find the evenings to be a "special time" in Monterosso and I always enjoy that time.
All of the five towns are trying to find ways to deal with the severe overcrowding that seems to be increasingly common, and hopefully they will find a solution. The C.T. is perhaps my favourite part of Italy, and these problems won't keep me from visiting there.
Good luck with your decision!
