Of the places you mentioned, we dove Key Largo, Looe Key. Key West and West Palm beach.
First, I'm not sure why you want to dive the Keys, but IMHO, West Palm Beach was some of the best diving we did in FLA. Don't know if you have given any thought to just diving there as it is where you will be, but if you haven't - give it some thought - it's great drift diving with lots of critters! I would highly recommend Diving Solutions as an operator. Solid operation.
http://www.divingsolutions.com/
As for the Keys, here are our observations and thoughts.
In Key Largo, we have to second the recommendation for using Blue Water Divers. Board member "KeyLargoBrent" works for them. We dove with 6 different dive ops in FLA and thought these guys were the best. It's a smaller more personalized operation and I'll guarentee you'll enjoy your time with them. The whole time we dove with them, you got the feeling they were out on the water because they wanted to be there - not because they had to be there. You can tell they love to dive as much as most of us do. If you enjoy wreck diving, you should really "do the grove" - just the size of it is amazing. It can be a tough dive though, so if you haven't got a lot of experience, take a DM down with you - we did!
Looe Key, as mentioned, is a great place to watch the critters. It is a very relaxing day of diving in relatively shallow water. You max depth is around 25ft so you are in for an hour on each dive. The diving is very easy. You just swim up and down the finger reefs so navagation is a breeze. You will see tons of critters in the area and the reefs are in decent shape. We dove with Looe Key Dive resort:
http://www.diveflakeys.com/
We did the Wednesday dive which also includes the Wreck of the Adolphus Busch. It's a very easy wreck dive and worth the effort of going on a Wednesday or a Saturday. You will find a Goliath Grouper in the wheel house that is simply massive! The operation itself is a bit of a cattle boat so if you don't like crowds - stay away from this one - they take snorklers out to the reefs as well since they are so shallow. Otherwise, we had a good time and would repeat with them.
Key West was a big disappointment. The diving was mediocre at best. The vis was poor - only about 25ft and the reefs were unimpresive. They are in bad shape - pretty banged up from years of bad divers. We also didn't see nearly the marine life we did in other locations. We dove with South Point Divers:
http://www.southpointdivers.com/
They are a state of the art operator with the best dive boats and best equipment. The only thing we found unimpressive with them was they were definitely "working". They seemed to have little interest or enthusiasm for what they were doing - they were there for the money and you just got the impression they didn't want to be there. Having said that - I would recommend the op - they certainly got the job done.
As for Key West itself - we love it. Certainly not the place to be if you are homophobic - but definitely an all around fun place. We just enjoy the carnival atmosphere of the place. Downtown Duval street on a good party night is an experience you won't forget - an thats what life is all about.
As far as accomodations - we did the basic Days Inn thing so not much to report there - clean and reasonably priced. I'll defer the accomodation recommendations to the others as I;m sure everyone knows all they need to know about the Days Inn chain and others that are similiar.
Cheers!!!