The Casino at the Wyndham El San Juan as well as this beautifully restored hotel, is a great place to stop. It is about a $10 taxi ride from the pier. I am not a gambler, but this site is gorgeous. Just stop for a drink at their Lobby Bar and people watch. a self guided walking tour up to El Morro is very nice. Go to the pink Information center at the beginning of LaPrincessa for a pocket sized walking map which will point out all of the historic sites. There is also a free Trolley paid by the merchants that can take you up the hill to the Fort.
I have been to St. Thomas numerous times and we try to do something different each time we go. Both San Juan and St. Thomas are very easy to do on your own by walking or taking a taxi. Options: Maegan's Bay, Sapphire Beach, Coki Beach and Coral World. a 3-4 hr. taxi tour of the island to include stop especially Mountain Top - home of the Banana Daiquiri. I always allow some time for late afternoon shopping at Havensight, if I don't want to go into Charlotte Amalie.