I'm just returning from diving last week and did the same thing you are going to be doing. We have never dove the Keys and had a great time.
In Key West, I originally was schedule with Dive Key West, but it was cancelled due to not enough people on the boat. We went w/ Southpoint and the trip was great. We did one trip w/ them.
Innerspace is a great six-pack operator - Robert was the captain and you can't go wrong w/ them. They are on Big Pine Key and go to Looe Key Reef. We made 3 trips w/ them and will return next time when in the Keys.
Captain Hooks was also good, w/ great people and great dives. They are at MM 53.5 in Marathon and will also get our business again. We dove w/ them for 2 days.
At MM 90.5 on Plantation Key we went w/ Florida Keys Dive Center for upper Keys diving. We enjoyed them a lot and dove w/ them for 2 days. Also highly recommended for that area was Rainbow Reef Dive Center.
We stayed at Sombrero Reef Inn in Marathon - it was a 1 bedroom apartment, so we saved money on eating out.
We enjoyed out trip w/ 18 dives for the week.