Raj, flight is like $109 USD (per person/round trip) and takes 20 mins. The boat is a $20-25 cab ride over to the boat dock and the trip is around $17 USD (per person/round trip) and is aprox 1 1/2 hours depending on the stops. Can sometimes be bumpy. Then don't forget the $20-25 to get back to the airport.
I suggest, depending on how long you'll be down, to either take the boat one way, the flight the other way or just the flight.
How many people in your party? How long will you be down?
Raj take the plane,great views of reef and bay. and quick 15 min.. If you go by boat? And it rains the day you go by ,or winds comes up ?? can be nasty.Does not start your trip in the best way..just my opinion . Go live the dream and enjoy.
We generally tell people to take the flight over to San Pedro, and then take the water taxi back if they want....less hassle, less tired, (usually having flown all day, adding another three hours and several luggage transfers later) it is much easier. Local airline employees will help you with bags from the time you get through immigration.....nothing for you to do but get on the plane, and pick up your bags in SP.