la perla has some nice spots
We stayed in a hotel called El Convento in old San Juan. It was very nice and not too pricey at the time - old school 3 story hotel that surrounds an open courtyard. Cool place in a great location.
There have been several PR threads over the last couple of years. You might want to search for those for more info.
I'm a big PR fan. Love almost everything about the place. You need to plan carefully with such young kids, though. PR has plenty of crime and once you get away from the big cities it's very rural with few English speakers. But if you take basic precautions you'll be fine.