Bad operators don't stay in business in the Keys very long..... too much competition.
Given your profile indicates you have less than 25 dives, I recommend Key Largo and Rainbow Reef. There are lots of beautiful shallow reefs in the upper keys that are perfect for your experience level. Look at RR's webste: all the reef trips are to sites that are nice to great. RR puts guides in the water which is nice for people that are unfamiliar with the sites: there is no extra fee for the guides. I usually dive with RR once or twice a year. The only downside of RR is that it is a popular shop with good service, so the boats are usually full. They've got big Newtons so there's still some elbow room, but not a lot
My main dive operator is Conch Republic Divers whose main boat is also a Newton.... they are really good for divers that are more independent/experienced or simply don't desire a guide. They also go to sites other boats don't hit quite as often given their location. I usually dive with CRD three times a year.
I've dove with Islamorada Dive Center a couple of times. They put guides in the water too. We went to deeper reefs on the trips I've been on, not sure that'd make much sense for you. They seem like a good outfit.
If you want a six pack, try Quescence. Good people and good shop, but I don't use them much since I don't like small boats.