I lived in Islamorada for quite a while and worked in Key Largo. Both areas have good dive operators. If you are staying at a resort, and if that resort offers dive services, then it is often more convenient to use their services.
I personnally like to Dive from Key Largo because there are a wider variety of services and operators available. But I think that as far as quality of service and access to good dive sites, they are about the same.
Personally I used Amoray, Divers City or Slates Atlantis when I went out of Key Largo.
If the weather fails to cooperate or if you just want to get in and do a "tune up" before heading out to the reef, Key Largo also has a place called Key Largo Undersea Park (Home of Jules Undersea Lodge) which is located on Shoreland Drive. It’s a sheltered lagoon that is set up for diving including a dive shop, equipment rental, air, etc...
Where ever you go, it’s bound to be fun...