Tourists can rent a private shuttle but in my opinion the public boats are just as good. They are much cheaper and it's more interesting to do what the locals do, which is catch a boat at the public dock and take it to whatever village you're going to. It's like a public bus system, only with boats.
Each village has its own dock, with boats leaving frequently. The workers are very helpful in answering questions about timing and distance and location. You just hop on and enjoy the ride.