A few thoughts:
1.) I tend to hear the upper Keys endorsed over the lower. I've been to Key Largo;
trip report if it's of interest. Rainbow Reef Dive Center moved their location a bit since then.
2.) I was quite happy with Rainbow Reef Dive Center and would use them again. If you like a big, fairly stable boat, no-added charge guide service, option for 2 2-tank trips (4 dives) per day with a cheap package deal option, it's really sweet. They're reputable on Scuba Board, based on reports by a number of people.
3.) But, if you like small, 6-pack boats, don't want a guide, you might like Quiescence, which I keep reading good things about. Same region, but an apples and oranges comparison. Who's best? Who's judging?
4.) When I dove in 2013, the morning boats had 2 options; 2 shallow reef, or a deep wreck followed by a shallow reef (or a 2nd deep wreck dive). Saw 2 guys have to sit out a deep wreck dive because they didn't have AOW; Captain asked if they had log books (to show deep experience, I think), and they didn't. Your profile says you've got under 25 dives. If you don't have AOW, you could take the course with Rainbow Reef and still dive a deep wreck.
5.) I'm surprised I haven't seen more on the thread about Conch Republic; never dove with them, but they get very consistently positive reviews on Scuba Board.
Richard.