If you're speaking of the "5-Star St. John + Trunk Bay" we did that excursion from St. Thomas and LOVED it. That's the only way we've been there so I can't compare it to taking the ferry yourselves. The ride there on the Leylon Sneed is incredible + very well narrated. The beach at Trunk Bay is drop dead GORGEOUS. Then you return to the Leylon Sneed for a limbo contest and free rum punch all the way back. All the snorkel equipment is furnished. You can either swim to shore or ride the motorized inflatables. Highly recommend this excursion.
Leylon Sneed picking us up from pier.
Trunk Bay beach, you snorkel a reef to the right of this pic.
I must agree with Cleveland Rocks as it is a wonderful tour and Trunk Bay is as beautiful a beach as I have ever seen. However, (in my own opinion), you should do the ship's tour because it is very well done and I think Trunk Bay is just too far away to take a chance doing it on your own.
Carnival Liberty New Year's Eve 2007
Liberty of the Seas 5/2008+11/2009
Allure 1/16/ 2011
Vision OTS 2-14-2015
Freedom OTS 3/6/16
Having done it myself, on our own, I would suggest just doing the ship excursion. Yea, you may save a few dollars, but there is a good deal of time involved in getting there and back, it would be nice to just sit and have someone else handle all the details. There is also the cost of a taxi to the ferry and another one once you get to St. John...
Either way you go, just go, its a beautiful island and you'll love the beauty.