You will probably get lots of replies & opinons. If you go back to older posts, you'll see many ideas as well. But some of the major things would be: Definitely go to St. John to snorkel when you are in St. Thomas. I think your kids will enjoy this a lot. This island is STUNNING! You see other, smalling islands all around on the trip over. This is one of the ONLY ship tours we usually do, just to save time, but you can do it on your own as well. Just take a ferry from either Charlotte Amalie or Red Hook (you'll need a cab to Red Hook, which makes for a shorter ferry ride, but the ride from Charlotte Amalie is beautiful). Catch one of the open jitney buses for a ride to Trunk Bay, where the beach is georgeous. There are showers & snorkels for rent. It's a nat'l. park. & very well kept. Be careful of your time, though, if you are on your own. There are also jeeps for rent on St. John, not far from the dock. So you could drive yourself along the road to Trunk Bay. There are many nice beach stops & GREAT views along this road. But again, if this is your very first time there, I think that's biting off kind of a lot.
The tour is a fast way to be sure & have time to shop or see other sights in St. Thos, however. Many people say to go to Magen's Bay, but we were quite disappointed the only time we were there. If you go to Puerto Rico, just walking around the Old Town is fun. It's well kept & very historic. Also the forts. You can pretty much walk everywhere there. Go to a store called "The Butterfly Store" near McDonald's. It is REALLY neat! Anyone can tell you how to get there. Going to the rain forest takes a LONG time & unless you are dying to see tropical vegetation, not worth it for such a short stop. In St. Maarten the shopping is as good & maybe better for several reasons than St. Thomas. (There is a fun store called, "Mango in Paradise" that sells lots of crazy Jimmy Buffet stuff.) Crowded, but not as bad as in St. Thomas, & you don't walk as far. We once stayed a week on St. Maarten, but we drove everywhere. The tours are rather high & the cabs are not all that cheap. There are some little beaches near downtown, but it is almost a must that you need to somehow get over to Marigot to see the French side. Do not go on the sub ride/tour of Marigot. We did this w/friends a few years ago & there just wasn't much to it. We even complained to RCI because the tour wasn't exactly as presented. (For the record, we got free bottles of wine.) However, your kids are going to have the most fun either on one of the sailing excursions or at Orient Beach. (You'll have to take a cab or minivan tour you can arrange yourself.) They have parasailing & all sorts of beach activities & restaurants & things. (You could also arrange for room service to bring you sandwiches & fruit to take w/you for a picnic so you won't have to spend $ on food.) Also the beach is for nudists at one end. (You can ask to be dropped off a little further away from it if that's a problem, but you must be prepared that a nude person could walk by. Also toplessness is fairly common. Just thought I'd mention that incase it would be an issue. It becomes less distracting than you'd think.) I know you'll get more posts on this, but hope this helps some.