One fun activity geared to families with kids of (almost) all ages is horseback riding in the rainforest. It isn't really much of a 'lush' rainforest, but the horses are good and the path easy to go on. The ride lasts for a couple of hours, with a stop midway through by a creek which enables all weary riders to take a dip in a (very cold) creek. Kids like it, and parents generally don't go in. Be prepared with a bathing suit, towels, and definitely sunscreen lotion. A hat would be a good idea. Given that it is a rainforest, having a poncho, or basic waterproofing, also makes sense.
The Westin hotel in Puerto Rico can help you arrange all types of activities ( and is a fabulous place to stay for a family (but pricey).
Also, a perfect activity for kids over 8 years of age is underwater helmet diving. They will love exploring the underwater world, walking on the bottom of the sea wearing a helmet. It's a unique activity available just minutes away from Old San Juan, on the beach right behind Hotel Normandie. When they can imagine playing a frisbee underwater? And they learn also about the history (Bateria Escambron and Old San Juan City walls) and the marine life. Bring your bathing suit and towel.
Try it with Sea Trek San Juan www.seatreksanjuan.com .