If there is just the one of you then without question fly to San Pedro directly from the International Airport (assuming that's where you're starting from). If there are four of you you can save money, but not time, but taking a taxi to the Municipal Airstrip and flying from there. fares are about half, but the taxi ride is expensive. If you're arriving from overseas I don't recommend taxiing to the shore and taking a water ferry. You'll save money but it'll cost an enormous amount of time and add personal stress.
If flying, always book in advance. That way the airline (Tropic at any rate) will move heaven and earth to get you to San Pedro that day, even if your incoming flight is delayed. But not if they don't know you're coming.