I've not heard of a water taxi either.
Personally, I would either book it through an independent company, such as Shore Trips, just to mention one of many, because it'll be alot less crowded. Or I would simply hire a taxi so I could do my own thing on my own time and not have to worry about being in a large group of people waiting for all of them to do their thing.
When we hire a taxi we make sure we agree to a fare before we get in the cab and then we don't pay them until they've picked us up and brought us back to the pier. Have done it many times in Jamaica and have never had any problems. But we'll usually walk outside of the gated area so we get better rates. (Taxis inside the gated area have to pay a fee to be in there, so they pass that charge along to their passengers.)