My husband did the BOSS in St. Martin and in St. Thomas on two different cruises. I tried it but I was too claustrophobic to do it. He loved it, though. It's like a little scooter with a bubble helmet above. You go under the water and come up into the helmet (they give you about a half hour of training in a room first). Then the guide takes maybe 6 or 8 of you down at a time, leading you along and pointing out coral, watching fish go right by your face, etc.
There is a lot of shopping in St. Thomas as well, my only suggestion being that if you're looking for something in particular, be it perfume, jewelry, electronics, etc., know what you can get it for at home before buying it in the islands.
In San Juan, a trip to El Moro fort is always interesting as part of your day.