San Juan is definitely one of my favourites! Probably because I love to eat and Old San Juan has some amazing restaurants. I think if it is your first time to San Juan it wouldn't hurt to fly in maybe a day or two earlier. If your lucky enough to be there for the night then definitely look at this one Night Tales in Old San Juan Walking tour - Legends of Puerto Rico, Inc. they do a night walking tour of San Juan which is great. Really informative, saw some great places, beautiful pictures and the guide was fantastic.

I also did the bioluminesct kayak trip there which is not in San Juan, a couple of hours out of town but was one of the most magical experiences I've ever had!