While in St. Thomas, if you just want a "beach" day, take a cab to Meagans Bay, very calm and pretty beach, no snorkeling there though. If you do like to snorkel, I'd take the Red Hook Ferry over to St. Johns/Trunk Bay. The island of St. Johns is truly a paradise and the snorkeling is pretty good at Trunk bay. Its also very easy to do on your own, takes a little traveling time, but well worth it. You can split the day between going there and getting back and doing some shopping. The Havensight mall is right by the pier in St. Thomas and has the same stores you'll find downtown.
If you haven't already visited the old forts in San Juan, thats always worthwhile, you can walk from the pier. El Morro is definitely something to see at least once, a lot of history there. Have a fun cruise.