There is a tour at St. John that takes you around the island and includes about 90 minutes at Trunk Bay which I highly recommend.
In St. Thomas, Megan's Bay is a large beautiful beach with great sand and the clearest water! Lots of shallow areas to swim w/ no seaweed or shells to step on! Pretty little fish swim with you! The mall in St Thomas is a lovely indoor/outdoor type and very clean with reasonable, friendly shops. Visit Hard Rock there for great food and service (tshirts too of course!) Skip the straw market at St. Thomas unless you like cheap tshirts, crowds and sweating.