We once did an excursion on the "wild thing" that landed us at Trunk Bay, but they don't always go there, we were very lucky that day. We've also just taken the Red Hook Ferry there on our own, its really very easy to do yourself. I think as long as you get a chance to snorkel over there, either one would be good. Its definitely worth the time and effort to get over to St. Johns, very beautiful island, so go for it!
St John is beautiful , there is no doubt about that. Getting there and back can in fact be a little bit of hassle. Nothing terrible, but certainly not as conveient as if it were on the same island. Let me suggest Megans Bay It will be crowded, but it is a huge beach , just keep walking until the crowd thins out. Saphire and Coki are also popular alternatives.
We were in St Thomas last January on the Triumph and they offered a sail & snorkle excursion. Only 6 passengers on the sailboat with 2 crew. We enjoyed a lovely sail and some excellent snorkling at Buck Island. It was a wonderful morning and having only 8 people aboard was heavenly.
If you want to snorkel at Trunk Bay I recommend that you go on your own. The excursions do not spend much time there at all. If you go on your own - you decide how much time you want to spend there. When we did it in August the taxi, ferry, taxi process was very easy. I hope this helps!! Feel free to email me if you have any other questions.
Everyone should see Trunk Bay on St. John at least once on a cruise. However, getting there takes anywhere from 1.5 to 2 hours to get there on the ferry and bus ride to the beach.
There are many beautiful beaches on St. Thomas as well. I am going to try Megans BAy on my November cruise.
Hope you have fun!!