It's kind of hard not knowing your certification levels for recommending dives, but...If you are staying in the Marathon area to dive, then the Thunderbolt is a can't miss dive! (deeper wreck at 120 to the sand) The reefs in that area are decent The Donut, the Stake, Sombrero light...all nice places to dive and plenty of fish! (I always use Captain Hook's or Tilden's in that general area)
If you are venturing out towards Key West, then you can take a stop in Big Pine and dive Looe Key reef which is one of the nicest reefs I've seen. (the Adolphus Busch is there, but is just an "OK" wreck dive..although Loos Key Resort does a Wednesday 3 tank dive, One on the Busch, and two on the reef...great deal if ya ask me!)
Further down in Key West, you can dive the Vandenberg, I've used either Subtropic or Captains Corner down there. The reefs off of KW aren't bad, but there are many better reefs down there!
If you are headed up towards the Islamorada, Key Largo area, there are more wrecks and reefs than you can shake a stick at...I've been using Conch Republic Divers exclusively the past few years, you can't go wrong with them!
Good luck! Enjoy and safe diving!