The upper keys is the best. You'll also find that operators that are 20 miles apart cover different dive sites. There are more dive sites off Key Largo, and some of the best, too. You might want to decide if there are specific dives you want to make (wrecks in particular) and find an operator that covers that location.
I don't think there is a bad operator in the keys. I've dove with three, and would go back to SilentWorld my next time down. If you plan on doing a lot of dives, they are the most reasonable and they have small relatively fast boats.