Last time we were in St. Thomas we took a bus (very inexpensive) to Magen's Bay and spent some time on the beach. Later we went up to Paradise Point to view the island and ocean and have a quiet cocktail at the end of the day. Every time we had come into port we would say, "we should take the ride up for the view"; it was worth the time.
In San Juan, depending on time, a ride up and around the forts is very nice and you can jump on and off the ride along the way and see a little of Old San Juan at the same time.
Enjoy your cruise !