One our trip, time of arrival was the decision maker and you should consider your arrival time. If you had a early arrival into BZE then the water taxi might be more attractive since you room might not be ready when you arrive in AC. Of course there is always a cold Belikin waiting somewhere. The flight is more tourist friendly. Also if you are planning any land based tourist activities you will be taking that boat ride in most cases and the view on the flight to AC is awesome.