(Edited - this is RumBum writing in Chris's account...)
We went to PR in 2004 so some of my info may be outdated. But here goes.
-Beware of El Conquestador (hotel) and their dive shop, Casa Del Mar. They were UNSAFE and destructive to the reef.
-There really isn't any diving in San Juan that we found.
-If you are renting a car in San Juan, buy the best auto insurance they offer. Those people make Houston traffic look downright tame. (Seriously!)
-If you're going to be on the East side (Fajardo area) you should look into diving Culebra and Viques.
-Definately kayak out to the Bioluminescent Bay. It's an experience you will never forget!
-Some cool sit intervals are the Bacardi Factory, Aricebo museum, and El Yunque National Park.
-I liked the diving on the west side better. Candyland and Sea Fan City were amazing.
-I've heard that the South is good too, with Paraguera divers. Black coral walls out there. Can't speak from my own experience though, we didn't make it that far south.
-I highly recommend Oceans Unlimited as a good operator for west side diving.
Here's a cool link for PR operators and sites:
The complete Puerto Rico scuba diving guide covering dive sites and dive centres
Hope this helps!