I've dived in San Juan, PR.
By Caribbean standards, it is a 1 on a 1-10 scale.
By New Jersey standards, its a 3.5 (because the water's not so cold).
Expect visibility to be poor and the water green. San Juan harbor puts out a lot of silt/sentiment and has pollution issues. The best diving in PR is a few hours East, a few hours West, or a half day to the Southside.
San Juan is IMO the worst possible place on the island. This pretty much is why you're not finding many shops recommended.
Thus said, when I suffered a dive there in 1998, we used Carribe Aquatic Adventures who at the time was operating out of the Normandie Hotel. I understand that they still exist, but since I was very dissatisfied in the service we received from them (they changed our reserved boat dive to a shore dive, offered no reduction in price *AND* then showed up a half hour after the appointed time), I still would not recommend them.
-hh