We have been there a number of times (both cruise and land-based vacations)and really love St. John and Trunk Bay, but I have to agree that it gets way too crowded on port days. Since you want secluded beaches, a great way to get there is by a charter such as recommended by cycofan on a small boat that will get you to beautiful little coves and beaches that are far less touristy. If you don't mind a power boat (as opposed to sailing) and price is no object, you can charter one for 1/2 day and still have time to see some things on St. Thomas, such as Magen's beach, and the beautiful vista points.