Hi Kim,
I have a few ideas in mine for your pirate! First, if you do not mind splitting up, he can go on the
Pirate Adventure at the Grand Floridian. Here he would spend time with other pirates looking for treasure. You could go to the spa or shop.
If you want to do something together, would you consider a tour? I took a backstage tour with Disney and it was wonderful. Two tours which might be of interest are the
Disney Family Magic Tour where you would go on a scavenger hunt of the park. Kara on this panel did this, and she loved it.
Another tour, since your son likes animals, is in EPCOT and is called
Seas Aqua Tour. This tour would have you in a wetsuit and up close with the marine life.
Unfortunately, there are no separate tours he could take at Animal Kingdom because he is too young.
I hope this helps and have a great trip!
Beth