Well, I just booked a San Juan hotel for one night next June. I agree, anything that looks good is expensive. I plan on trying Priceline "bid a room" thing once we get closer to our cruise fate.
Since you are going to be there for a longer period, consider staying outside of San Juan, maybe the hotels further away are more reasonable? I couldn't justify the expensive taxi ride from the airport to a hotel not in San Juan and then back to the ship for one night, but if you can save $300 on hotel costs, it might be worth it.
Carnival Cruise Lines:
Fantasy 90, Celebration 95, Victory 05, Conquest 05, Spirit 6/06, Freedom 6/08, Holiday 7/08, Victory 6/09, Valor 9/09, Dream 6/10, Splendor 8/10,Conquest 8/11,Magic 11/11,Triumph 4/12,Spirit 7/12,Freedom 11/12, Triumph 2/13 - The fire cruise
NCL Dream October 2006, RCCL Mariner OTS June 2007