Here is some information I got online. I would call and not tell them you are going to be on a cruise ship, it seems the cruiselines are getting wise to us booking our own tours, and they are losing out on some money.
If you really want to get to the bottom of it all, board the air-conditioned Atlantis submarine, which takes you on a 1-hour voyage (the whole experience is really 2 hours when you include transportation to and from the sub) to depths of 90 feet, where an amazing world of exotic marine life unfolds. You'll have up-close views of coral reefs and sponge gardens through the sub's 2-foot windows. Atlantis divers swim with the fish and bring them close to the windows for photos.
Passengers take a surface boat from the West Indies Dock, right outside Charlotte Amalie, to the submarine, which is near Buck Island (the St. Thomas version, not the more famous Buck Island near St. Croix). The fare is $79 for adults, $39 for ages 4 to 17; children ages 3 and under are not allowed. The Atlantis operates daily November through April, and from Tuesday to Saturday May through October. Reservations are a must (the sub carries only 30 passengers). For tickets, go to the Havensight Mall, Building 6, or call tel. 340/776-5650.