Tortola- definitely the most popular and worthwhile excursion is Virgin Gorda and the Baths.
St Thomas- I actually enjoy coral world, it's just an aquarium with places to see the natural water as well, coki beach next door is pretty nice too. I also enjoyed seeing blackboards castle (more of a turret) also shopping downtown is decent. Magen's Bay will be touted as one of the best beaches in the world, but it's honestly a little crowded these days to truly enjoy it, but nice to see from above. Paradise point and the sky ride up have a beautiful view, plus it's within walking distance from the ships, but it's pricey to get up there and the food up top is mediocre, However they do claim to be the inventor of the Bailey's Bushwacker (basically an alcoholic frosty)
St John- Beach, beautiful beaches, some of the nicest i've seen. Trunk bay is the most popular, and a beautiful site, Also i've heard good things about the old sugar plantation.
All of these islands are solid for ecotourism as well, zip lining is very popular in St Thomas due to it's mountainous terrain. Taxi's are always readily available in St. Thomas, my first trip there we just hopped taxi's and explored. Great snorkeling spots in all 3, parasailing and party boat/ snorkeling excursions are all good bets as well.
Also, if you do choose to ferry over to St Johns from St Thomas allot at least an hour each way, it's about 20-30 minutes to the ferry port and about a 20 minute ride to St John's from there.