My favorite small op in Key Largo is Island Reef Divers. Skip runs a six-pack that is fast, he's very flexible and knowledgable about the various sites and which sites are best given tides, currents, weather, etc. He can arrange for a guide. He also has the best prices from the shopping I've done.
I heard great comments about Tavernier Dive Center, and went in there last summer to possibly book some dives. The staff in the office did not seem very friendly or helpful, and basically made it clear that they were going where they wanted to -- not me! I also looked around their shop and saw their boat come in -- with about 12 divers on it and looking a bit cramped. So, while I haven't dove with this op, I thought I'd offer a different point of view than the rave reviews I see posted here.
Scuba legs