We have done this 2x in the past 10 years and plan to do it again on the Rotterdam in February.
In the past the taxi driver on St. Thomas had a buddy on St. John waiting for us and he took us to Trunk Bay and picked us up. He then called his St. Thomas buddy and told him what ferry we were on. He was waiting for us at Red Hook If you are cognizant of the time, this is definitely the way to go, as you can twice as much time on St. John vs the cruise excursion. It's really easier than you think, plus the ferry ride is usually quite calm and pretty.
