If you're landing in San Juan, you're going to be smack dab in the middle of the tourist trap so Besides El Yunque Rainforest, which is maybe 40 minute drive away, you'll be jammed with traffic....
But if you do go to the El Yunque Rainforest....Go to the waterfalls.....then when you get back to main road #3, make a right and go a couple minutes and hang out at Luquillo beach....Sunday is the best day to go to the beach and that's the most popular and peaceful one....
Ah, just thinking about it brings me back to the good ole days of living in Puerto Rico.
Or skip all of that shit and when you rent your car in San Juan, drive three hours to the west coast and you'll have a great time.....Focus your time in a town called Aguada which means "Give Water" in Spanish and the next town over, Rincon, the laid back american surfer type spot...It's a wonderful place and not touristy at all like you're going to get in San Juan...
I have a favorite little hotel that I stay at when I was on the West Coast.........Damn I miss it.....I woke up and walked out of my balcony to this every morning...
More pics and my story of my visit there way back then can be found at.
http://www.mrnogood.com/travel/puertorico.htm