You will have enough time to get your snorkeling in but if you stay on St. Thomas and snorkel at Coki or swim at Magen, you avoid the time lost on ferrys and are not limited to their schedules.

IMHO, that makes for a more relaxing vacation given the limited time you have off ship.

If your heart is set on snorkeling St. John try one of the day sails. We have booked two that both say they will accomodate the cruise ship schedule on their web sites. This will cost you a lot more than the ferry or a cab ride but it is probably more reasonable to book it independently than through the cruise ship. You can try Ike Witt - Captain Pat here is the link:
http://www.ikewittcharters.com/

Or the Alaunt with Captain Ron and Carol here is the link:
http://www.alauntcharters.com/usvi_daysail.htm

My only comment regarding getting from St. Thomas and St. John would be if you are on a tight schedule it may not work simply due to the ferries not always running on time and sometimes not running at all. When we were there last month we were at Red Hook waiting to go to St. John on the 9a.m ferry. We lined up at the ticket booth and the line stretched all the way to the ferry dock itself. 9:00 came and went, 9:15, 9:30, 9:45, finally at 9:50 someone said "just get on the boat, get on the boat, you can pay on the boat", so everyone in the back of the line were the first ones on but fortunately there was enough room for us.

Leaving St. John 2 weeks later we wanted to take the Charlotte ferry to enjoy the ocean vs. a cab and we waited and waited for the 11am ferry, it never showed, then around 12 noon a boat showed and they said just get on, well everyone rushed the boat only to find out in only held 40 people, so everyone else was left there to wait for the 1pm (if it shows said the dock person), or take the Red Hook of which we did and then were in a van for 1/2 an hour.

So if you are on schedule you might want an alternate plan such as using some private charter.

Fortunately we were on "ISLAND TIME" so we didn't care about the mess up on either end but some people were mad as heck!

Gail: If you have only 6 hours in port, do you want to spend at least 2 of them in transit? Quite honestly, I would save the commute for your next trip to the Virgin Islands, when you need something to do for 7 days! 😉 There are great beaches on St Thomas and Water Island with much shorter travel times, also day sails.

Jill: We had a similar problem last weekend. We wanted to do some errands and have lunch on St John. We sat in line for the 11 am ferry till 11:35.

Not to start another debacle like the one over St John/St John's BUT the capital of St Thomas is Charlotte Amalie. Charlotte is in North Carolina! 😉 People call it the "Town Ferry" as opposed to the Red Hook Ferry..