so much depends upon what you want to do or want to experience. Some suggesstions.
San Juan - take a walking history tour of Old San Juan that includes the city and Fort El Morro. It is very interesting. Or take a tour into the rainforest- this is beautiful. Or just hit the beach
St. Thomas - beautiful beaches with turquoise waters and white silky sand. You can do St. Thomas very easily on your own. There is very good snorkeling to be experienced over on St.John Island - you can get there on your own, or if you want a treat then book the Champagne Catamaran sail. If you want a great beach on St. Thomas proper then i would suggest Sapphire Beach. There is very good shopping either at Havensight Mal or in downtown Charlotte-Amailie. The Paradise Point Tramway is also a fun thing to do, its a short walk from Havensight, the tram takes you up the mountain, the view from the top is amazing- there are shops, restaurants, and a beautiful flower garden up there.
St. Maarten - we did the Golden Eagle Catamaran sail and totally loved it, you get to sail, you go to a lovely beach where you can swim, relax on the beach or do some snorkeling, and party on the way back. Another fun excursion is the America's Cup Regatta - you sail on racing sailboats in an actual race, we haven't done this one but know lots of folks you have and they had a blast. St. Maarten is also a great shopping port. You can either shop on the French side-you have to take a taxi from the pier or you can shop on the Dutch side - take the water taxi from the pier. Orient Beach is by far the most popular beach on St. Maarten - just know that it is french and it is topless and parts are clothing optional.
we did the atlantis submarine in st thomas, not really worth the $. in st maarten, we did a tour with a local taxi bus and PERRY took us all over including cokie beach for 25 minutes where we swam with schools of fish. cost $25 per person + tip great tour pulling over for foto ops.