Katie, those three you mention are great. Also take the tour of the Bacardi rum factory.
In El Yunque you can hike down to the waterfalls and swim there, but the water will be cold. When we did that, upon emerging we learned it had been raining for hours, but the canopy was so thick we never got wet.
Enjoy! And be on the lookout for el coquí.
I just came home from Puerto Rico on Sunday and I really enjoyed it, had never been there. We were only there for five nights, staying at the San Juan Marriott in the Condado area. Easy cab ride from the airport and we did not have enough time to rent a car and head out to the rainforest as was business trip for DH. We enjoyed an afternoon touring Old San Juan and the El Morro fort. We had some really outstanding dinners, both fancy and casual. The hotel was not a big resort-type hotel, more like an urban hotel but one with a beach and very nice pool area. There was a spa for massages and facials. What I liked was that you could easily walk out the hotel and have plenty of options for breakfast. There is a Starbucks right across the street as well as a cute Creperie. There are some shops to browse in. I would go back.