We went to St. John on our own last week. Here are my thoughts.
There really is not much time on St. Thomas and we tendered so it left us with even less time. We took a taxi to Red Hook which was an adventure in itself, DD3 was very motion sick when we got off. It took almost 30 minutes to get there and cost $8.00 per person. When bought tickets for the Red Hook ferry ($3.00 per person, $1.00 for the kids). The ferry ride took about 20 minutes and was smooth. It was almost 11:00 before we got to St. John.
There is also a downtown ferry from Charlotte Amalie to St. John. It takes about 45 minutes. We took this ferry back to St. Thomas and it was VERY bumpy. The lady in front of me asked a worker if the boat was going to tip over. A family who rode this boat over to St. John said that it was ten times worse on the way over. The cost was $7.00 per person and I think $3.00 for the kids. It was a beautiful ride and you got to see some incredible homes on St. Thomas.
We took the 2:15 ferry back to downtown and arrived at the tender station by 3:00. If you take the Red Hook ferry back, make sure you leave plenty early in case there is a lot of traffic on St. Thomas. There were seven ships in port that day!
St. John was beautiful! We walked to Mongoose Junction, had lunch, then walked to Gallows Point (we stayed there on our honeymoon and took pictures of the kids in the gazebo and hammock where we spent a lot of time while we were there). We shopped a bit in town and then it was time to return. It will probably cost you $85 to rent a jeep on St. John for only a couple of hours. Other posters have mentioned renting a car on St. Thomas and taking the car ferry over to St. John. That may be a less expensive option.
Beware of driving on St. John. You drive on the left side of the road. The roads are very narrow, steep and twisty. Wild donkeys and mongoose may cross your path.
I hope this info helped. Unfortunately, there is so little time on St. John once you go through the logistics of getting there that I am not sure you would get your money's worth out of renting a jeep there. Maybe choose a beach and take a taxi there to spend a few hours.
If you have any more questions, PM me.
Denae