My husband's family lives in San Juan so we visit at least once a year. It is one of my favorite places in the world to be!
I really like the Condado area of San Juan, particularly the San Juan Marriot. Beautiful beaches and lots of things in walking distance. I highly recommend renting a car. The traffic is intimidating and takes some getting used to but cabs and tour groups are outrageously expensive.
There are some great beach front apartments on Loiza Street (I'll repost when I remember the name) that are affordable, usually around $900 to $1200 per week if you wanted to do a rental home. Use caution with that though because most of the private residences do not have AC and it is HOT!
The rainforest and Old San Juan are beautiful but I would skip the Bacardi factory tour. Boring.
My 3 favorite places to eat are La Bombonera in Old San Juan, Bebo's on Loiza Street and the food shacks in Pinones. Yes, they are just road side shacks but sooooo good.
A word of caution...take bug spray. We were there in January and I was almost eaten alive. They are having one of the worst years ever with sand fleas.
Let me know if you have any other questions. I know a lot about the San Juan area but not much about the rest of the island. DH, however, is really familiar with all of it so I would be glad to pick his brain for you.
