Where to stay...
Well, I know this motel that is called the Green Isle Inn. It is not the best place, but the area where it is located is not bad at all. I don't have the number, but just make a search in hotels in San Juan. Its 5 min from airport, and its in the other side of the highway from Isla Verde (tourist area with beautiful beach, big hotels and casinos). I think the price is around $70 depending on season.
You might also want to check the Howard Johnson in Isla Verde. The price should be some more expensive, but I don't think much more. Spirit pilots used to stay there.
If you want to go to a better place, there's the Embassy suites, in Isla Verde. I have seen pilots from ATA and Continental staying there so I guess they should have good rates for airline pilots. When I say good rates, I mean around $125 and up for airlines. It's a very nice place to stay.
Good luck!
Scube.