Just got back from St. John and went on the jet boat. I took my two boys, while the wife watched. You can buy tickets just north of the dock, in a little shack that also has bike rentals, and other boat tours. It is a short taxi cab ride to the location, which cost us (4) $10.00 going and $12.00 back. They take any money, and will charge you based on the currency you used. It was about $39.00 each. It was a blast.
I highly recommend you bring a change of clothes with you if it is cold like it was for us, or at least wear something that will dry fast. Do not wear jeans!!!!! (Someone has to make the mistake) However, the taxi will take you back to the ship, and it is easy on and easy off the ship to get changed.
There is plenty of time to do this, and all you need is about 1 1/2 hours. They will call the taxi for you, however, it seems that the taxi's were roaming around the ship, and the "tourist" areas.
As far as making a reservation, we had absolutly no problem with this being booked, but it might have just been that it was 60 degrees, and I think the water was 40....