Hi lynne-
About three years ago my DH and I went to St. John's on our own from a cruise and loved it so much we went back for a full week the following year.
The logistics sound more difficult than they really are but I highly recommend doing on your own. I can't remember what time you can get off the ship in St. Thomas but we were one of the first ones off. We grabbed a cab waiting right off the ships gangway and asked them to take us to the Red Hook ferry. The ferry leaves Red Hook every hour on the hour. I think we were on the 9am ferry. It is about a 15-20 minutes ride to St. John and really a great way to get an overview of the beautiful island. When you get off the ferry there are many taxi's waiting to take passengers all over the island. Just ask one to take you to Trunk Bay (these are the open air taxis and sometimes wait for the cab to fill up--usually doesn't take long with ferry passengers). The taxis will frequently make 1-2 photo stops so you can get that gorgeous photo of Trunk Bay that you see in every travel magazine!!
Once you are at Trunk Bay there are changing/shower areas, snack bar, souvenir shop and snorkel rental. I think we were relaxing on the beach by 10am

The underwater snorkel trail was fantastic earlier in the morning but it got very cloudy by noon due to all the excursion people.
Our goal was to take the 2pm ferry back to Red Hook (4:30 all aboard, if I remember right) so we left the beach around 1:30. Lots of taxis waiting around to take people back into town (Cruz Bay). This is such a great little town to walk around and the people are sooo nice and friendly that we decided to take the 3pm ferry instead. We had a bite to eat and did a little shopping. Walked over to the ferry and back to Red Hook we went. (This was when we promised to return to this little island of paradise very soon...and we did!!!). One more cab and we were back at the ship by 3:45.
I can't remember the cost of all the taxi's or the ferry (6$ or close to it for the ferry) but I do remember seeing the boat come over from the excursions and feeling very sorry for those people who looked packed into the boat and then only having about 45-60 minutes at the beach. They also didn't get to spend any time around the island- which was our favorite part.
In case you can't tell I love this island. We are trying to decide where to go on vacation next year--Nov-2004-- and our family keeps talking about Hawaii but we would really like to go back to St. John and RELAX!!
Maybe someone else can help you with the two excursions as I have never been on one. If you have any other questions about St. John's just ask. I love to re-live this great vacation.