My wife prefers reef over wreck diving. Having said that there were more reef diving locations near Key Largo and not as many at Key West (which has some very nice wreck dives).
When we were at Key West, we ended up doing only one dive because of weather--and that was at famed Looe Key--30 miles east of Key West. We went with Strike Zone Charters at Big Pine Key. Of the dive operators that we used, they were the worst because the captain and crew were very unfriendly. The water was pretty choppy and the visibility was not great which was disappointing because the reefs at Looe Key National Marine Sanctuary are supposed to be fantastic. My wife wants to go back to do Looe Key some day and when we do it, we intend to book our dive with Looe Key Dive Center.
When we were at Key Largo, we had a fantastic time with Rainbow Reef and the dive concessionaire at John Pennenkamp State Park. I highly recommend them both.
When we return to Key West, my wife also wants us to dive Marquesas Keys--the only known atoll in North America. This cluster of islands is located 25 miles west of Key West and supposedly has spectacular, unspoiled diving.