I really like the El Convento Hotel (http://www.ElConvento.com). It is located right in the heart of San Juan's old section and used to be a Carmalite convent for centuries before turning into a hotel. It is somewhat expensive, but you will remember it forever. Great hotel (in my opinion)
Thanks for your quick reply. We are looking for convenience to the ship but also a hotel with nice rooms, good service, nice pool, etc.
I know we will be only there for 1 night but don't want to stay in a dumpy place.