Trunk Bay is a must see and do. Magens Bay is on St.Thomas and is nice too. I did that on my first visit and got a feel for the island etc. But now I usually go to Trunk Bay as I am comfortable with the logistics of getting there.
As you probably read it takes a taxi ride to get to Red Hook Ferry, then on St.John another taxi to Trunk Bay. Of course this is doing on my own and not a ship excursion.
Slightly off topic, but if you need any last minute items. The ship will dock at Havensight pier. At the back of all the shops on the left in same complex is Havensight Pharmacy. Have been going there for years, and grab myself a big ice cold Evian, bigger and cheaper than ship has for my trip to Trunk Bay.
If you do decide on Trunk Bay, get an early start. The ferry leaves on the hour. Magens Bay is just a taxi ride over the mountain, is beautiful, but not good snorkeling.
Best to you,