I've just taken the ferry over and then a cab to the beach, easy to do on your own. I've also done a snorkeling excursion that took us there as well. You do have a few options depending on what you want to do in St. John.
Has anyone used High Pockets or Island Girl to see St. John?
I made that trip on Fantasy with Capt Pam. Fantasy and High Pockets are owned by the same family...mother and daughter or some such. Both sail out of Red Hook. It was a great sailing day but you don't actually get to see a lot of St John. There is a designated anchorage and we got to snorkle over to the beach. There was a great lunch on the boat and then the sail back to Red Hook.
After tip and cabfare I think we spent about $350 for 2 people.
Two weeks ago we took the ferry over just to look around.
$24 pp round trip. I think next time I will take the ferry over and then a cab to Trunk Bay for swim/snorkle. If you choose to do that just make sure you have a long port day.
We have also used Castaway Girl (a ships tour) several times. It is a good and reasonably priced Catamaran snorkle tour if you have a shorter port day.