We did three tours El Yunque, a boat trip w/ snorkeling and El Moro.
I thought El Yunque was a waste of money. The place was amazing, but our tour sucked! It could have been that it started to rain, but it was so short and hardly had a chance to see anything! I think your better off taking a cab there and booking your own tour.
The boat trip was a blast. We went snorkeling in Fajardo.
Snorkel, Snorkeling and Sailing Excursions in Puerto Rico
We took a cab to El Morro and just purchased tickets there. No need for a tour package.