Depends on what you are looking for. The El Convento in Old San Juan is a great hotel and in a great location. It doesn't have a beach or a big pool, but I believe El Convento guests have privileges at a beach hotel in Condado.

If you are looking for more of a resort experience you could look at Isla Verde. The Ritz, El San Juan and Intercontinental are all nice hotels with great pools and on the best beach in San Juan. I've hear good things about the Courtyard in Isla Verde as well. Old San Juan is a $20 taxi ride away as well. However, my opinion is that most of the action in Isla Verde happens in the hotels and there isn't as much to do away from the hotels there.

Condado is a good choice if you are looking for a compromise between the two. The beach there isn't as good as Isla Verde, but the location is much closer to Old San Juan. As a matter of fact, you can walk to Old San Juan from Condado, though it is a fairly long walk. Also, don't make that walk during the night. Condado also has a lot of bars and restaurants located within proximity to all of the hotels there. La Concha and Marriott are both popular choices in Condado and The Vanderbilt is being restored. Not sure when it will be fully open, but I am sure it will be a very nice option.

Trip Advisor has a section in their forums about San Juan where you could also get a lot of good advice on hotels.

Have fun!