I've been to San Juan for the same time frame as you'll be there. We just took a tour after we got of the ship, there will be tons of tour operators waiting and it's maybe $10 -15 . Our guy took us to see new San Juan, a beach for a photo stop, El Morro and then to Old San Juan. El Morro will be closed but you can see the outside and get pictures. Even if you don't shop it's neat to walk around Old San Juan and see the churches,etc.
St Thomas the first time we went to Coral World, which I wasn't impressed with but many rave reviews for it, and Magen's Bay. This time we are taking a tour with Godfrey after reading tons pf great reviews for his tour. Magen's Bay is beautiful !!
St. Maarten we took a tour over to the French side and spent a little time there and walked around Phillipsburg. It was a cruise ship excursion so we were limited. This time we are planning to arrange a tour with one of the cabbies and maybe see a little more of the island.