St. Maarten is fun. The port itself has neat shops and all the transportation is right there. My advice is take the water taxi to front street and anjoy the shops and the beach. There are pleanty of other things to see and do, though!
St. Thomas is great. So many possibilities. We went over to St. John which was great. Lots of beaches and scenery. It does take a lot of time to get there, so, if that is not your bag, there is plenty to do in St. Thomas itself. Beaches, snorkle, shop. its up to you!
Not my favorite port but there are things to do there. You can find an excursion yourself or take one with the cruise line. You can walk around and go shopping, or you could go up to Fort Fincastle. The port itself is annoying as the have created a very small customs building where they make everyone go to leave and come back to the ship. It is very very annoying. Make sure you leave yourself at least 15 minutes to get through that nightmare on your way back. Also, Bahamas requires you bring your ID as well as your room key. LAME.