1.) When you get off the ferry there will be plenty of taxiis waiting. Ask one of them for an 'island tour', which is $25 p/p and lasts an hour and a half to 2 hours. They'll take to you to all the sights, stop for pics, explain the history, etc.

2.) New Horizons II does a great full day BVI. So does Captain Nautica. The Limnos is a little more 'family oriented', but still does a nice trip. Don't forget passports.

3.) I've never done any in-shore, only deep-sea (highly recommend DoubleHeader).

You can show up at the cruise ship dock at around 9am in STT, and there will be lots of taxis offering "island tours" to departing cruise ship guests. We took one on our first visit to St. Thomas (from a cruise ship), and it really was great. They went through downtown discussing the history of STT, went up to Mountain Top, stopping along the way for scenic pictures (and souvenier shopping from roadside vendor), and dropped you off at either Magan's Bay or back downtown for shopping. If you want to book something ahead of time, go to shoretrips.com. We used them on our most recent cruise to Western Carribean and trip was perfect. Well respected and they offer guided tours, both walking tour of Charlotte Amalie as well as the complete island tour. Good Luck!!!