If you are looking for inexpensive & no frills, try Holiday Inn Express (there's 2 of them, don't go for the newer expensive one).
We stayed there. It's nice, small rooms, has a small pool & continental breakfast. Again, no frills. You can book excursions right at the front desk. We paid I think like $79 a night.
If you go to Webshots.com, search for Cassie4486 and look for the cruise on Serenade of the Seas. I have a few photo's posted there of the observatory we went to. We literally had a private tour. It was just us and another couple and our tour guide took us to some of the local places & we ate at a local restaurant as well. Food was delicious! He totally went out of the way to show us different stuff that wasn't even included on the tour. I can't say enough good stuff about him!
As a FYI, if the hotel you choose has a casino, it'll be more expensive. I was told by one of the folks that lives in Puerto Rico about that.
Serenade of the Seas - '05
Sovereign of the Seas - '07
We stayed in San Juan last fall and stayed at Da House. Its a small boutique hotel in Old San Juan. We loved it and plan to stay there again any time we cruise from San Juan.
Celebrity Century 1/09
Carnival Destiny 10/07
Carnival Destiny 9/06
Monarch of the Seas 3/06
Carnival Inspiration 8/05
Carnival Miracle 4/05
Carnival Inspiration 4/04
Sovereign of the Seas 4/03