Hotel Milano is the most affordable, non-crappy hotel in Old San Juan. While it has small rooms that are nothing special, it is clean and in a great location.
I paid $125 (without taxes) for a room in the back. The rate includes a simple continental breakfast that is served at the rooftop restaurant, offering a view of Old San Juan and the harbor. The restaurant is also accessible to non-guests.
The receptionists were very helpful in organizing transportation, etc. Hotel Milano is a place for people who value location and not paying excessive amounts of money for accommodations over anything else. If you want a magical honeymoon experience, this is *not* the place. For that, try El Convento for about $400 a night instead. Their website is http://www.hotelmilanopr.com