If you want a guide, go with Rainbow Reef. They have big stable boats (good for a newbie) and good captains. Only issue is that they are a very popular operator and boats are usually full.
If you like a six pack experience, Quescence is a good option. Great staff and given there are only six people on the boat, you can probably name the sites you want to see. The downside is if the weather is rough the small boats can bounce around a lot (not good for a newbie). Also, there's no guide. The other long shot downside is that if you happen to get on a small boat with four other divers that are real idiots, if makes for a miserable trip since there is nowhere to escape to, like a flying bridge on a big Newton, in a small boat. That happened to a buddy and me a few years ago
I use Conch Republic the most. They have a big boat (similar to the ones RR uses) and it is rarely sold out. The staff is great and they will hit sites other boats don't get to as much since they are a little further south in the Upper Keys. Only downside is that there's no guide. On the shallow sites, a guide isn't really all that needed in my mind