Most of the Dive Ops in the Upper Keys get good reviews. My favorites are Blue Water Divers (Brent/Capt. Marvel), and Conch Republic (Gary/Brenda).
Blue Water does some Northern trips that are worthwhile. Conch does some trips farther south that are also nice. You may want to book a few trips with a N. Dive Op, and one farther south for some variety. All Ops go to the deep wrecks like the Grove/Duane/Bibb but one must be AOW to dive those wrecks, so keep that in mind.
We've stayed at several places. Ocean Point is NICE, but a bit pricey. Casa Del Mar is a bit outdated, but they have a great pool, and maybe it's been updated as it's been a few years since I've stayed there. One can get deals through Brent at Casa DelMar.
Rock Bottom prices can be had a Sunset Inn. The hotel is outdated, but very inexpensive (like $65 a night) and they have a nice pool. However it is a bit farther south, like 10 miles south of Conch Republic, around MM80.
We LOVE the Fish House, and always make a trip there for Dinner. Unfortunately prices have gone up over the years, so for a family of three, it's generally an $80 dinner unless one wants to skimp, and order lite/split meals etc., which is an option.
I would contact ANY dive Op you are considering and discuss what they do, and what you need to bring certification wise to dive the sites you are interested in. The Keys Ops generally require AOW to dive any deep wreck, and many will NOT substitute experience. Funny that as a diver with 1000 dives may get denied on a deep wreck while a diver with 11 dives just AOW certified is good to go....
Good Luck, and enjoy the trip.