I just got back from a long weekend in the Keys and used Conch Republic and Rainbow Reef. I like Conch Republic and had another great trip in their seldom crowded but big stable boat. Rainbow Reef was also enjoyable (on the big boat, at least). The staff is super and if you want a guide at no extra cost, they are a good option. Here's a dive report....
http://www.scubaboard.com/forums/florida-diving/488453-key-largo-islamorada-dive-report.html
Most of the bigger boats schedule site selection ahead of time. Most have on-line calendars and you can decide if they are going to places you'll like to see. Conch will let you choose a site if you are the first to book that particular day (I booked with the shop in early Sept and they let me choose 2 of the 6 trips).
I also have used Quiescence and they are a good option if you want a 6-pack experience. A little more expensive than some of the others, but if you want to choose your own sites and have a near private boat, this is the way to go.
Must see sites:
Shallow: Hens and Chickens, Snapper, Davis, Bentwood wreck, Mike's wreck and if you've never dove it, Christ of the Abyss (just to say you dove it: once is plenty)
Deep: Spiegle Grove wreck, Conch Wall reef, Eagle wreck, Duane wreck.
Hotels can be expensive and dirty in the keys. Ocean Pointe has nice condo rentals which may or may not be in your price range. If you want really cheap but micro-tiny rooms that are clean but in need of a coat of paint and general refreshing, you can try The Hungry Pelican. A buddy of mine and I just stayed there but spent no time at the complex except to sleep and watch the sunset of their dock. I'm not going to take my wife there since she's a bit more discriminating in her tastes, but when I make solo trips or trips with 'the guys', I'll stay again.
In the Marathon area, I did four nice dives with Dive Duck Key last year: all were shallow reef dives.
In Key West, I've been out with Captain's Corner a few times and will use them on my next trip in a few weeks. They make trips to the Vandenberg each morning: a wreck worth seeing.
I've stayed in a studio at the Conconut Mallory on Key West a few years ago and had a very nice experience.