That is quite a tight schedule to catch the 12pm boat and you might miss it. Typically it's an hour from landing to walking out of the door of the airport and a taxi is then a half hour drive to the Water Taxi Terminal. This only allows a half hour comfort zone for flight delays, baggage reclaim delays, customs delays, traffic problems etc. Just buy your ticket on arrival at the Water Taxi.
Further to Dianes point the Water Taxi can add four or five hours to an already long day if you are unlucky with boat departure times and arrive just as one has left. Are potentially five hours of extra travel worth the savings of flying to you? Many of our guests who are looking at this option do so not for budget reasons but as until reassured they wrongly assume the safety of the local airlines is questionable in a third World Country.