We did Trunk Bay on our own in December 2013. It was very easy, taxi and ferry prices are set, so do your research ahead of time. We loved St John, would go back there again in a second! We got off the ship as soon as we could and made a point to catch the 1 PM ferry back to St Thomas so we'd be back in time. We snorkeled and then got a taxi back to the ferry terminal and ate lunch at a restaurant right next to it.
There are taxis waiting at all locations to take you where you want to go, the ferry runs once an hour.