I agree the flight is much better than the boat ride. However, I also understand you having a fear of small planes. I am not afraid of flying in small planes, but do have a phobia that people have been telling me all my life to just not be afraid. Sometimes it is just not that easy.
The information I have included here can be found at this address: http://ambergriscaye.com/pages/town/quick.html
"Visitors to the Caye can also take a water taxi or ferry from Belize City to San Pedro. The trip, mostly on fast open boats with twin outboard engine seating 20 or 25 people takes about 75 minutes. On a sunny, calm day, it's a great introduction to Belize; on a rainy, windy day the trip can be wet and rough.
Several fast boats ferry passengers back and forth between Belize City and San Pedro, including Thunderbolt, Andrea and Triple J. Probably the most accessible boats are those in the Caye Caulker Water Taxi Association. These leave from the Marine Terminal near the Swing Bridge in Belize City. The Marine Terminal has a waiting area and two small museums to visit while you wait. Boats to San Pedro leave at 9 a.m., noon and 3 p.m., with a brief stop at Caye Caulker. Fares are US$12.50 one-way to Ambergris Caye. You disembark at Sharks pier in the middle of town. Fares just to Caye Caulker are US$7.50, and boats depart at 9, 10:30, noon, 1:30, 3 and 5. Children 5 to 10 go at half price; under 5 free. You can make reservations, but service is more likely to be first-come, first-served. A cab to down Belize City from the International Airport is about 20 minutes and US$17.50 for up to five people.
This is the cheapest way to Ambergris, approximately $15.00 U.S. one way. There are several to choose from, ask anyone when you arrive in Belize to direct you or take a cab. Everyone knows these boats. The ferry is is first come first served. The Andrea leaves at 3 PM. It is the latest ferry.
To get to the ferry from the airport, take a taxi from International Airport to Belize City. Taxis are available from the airport and in all towns. Rates are generally not posted in taxis. The airport is located nine miles from the city and is about a 15-20 minute ride."
However you decide to get to San Pedro I am sure you will have a great time and will want to return.
Hope this helps. Kathy