We're in the minority that prefers to take the water taxi - love watching the water change color as you leave the city, talking to the locals about the history of all the cayes as you pass them and getting that first look at San Pedro as it appears on the horizon. Also provides the first layer of my tan each year! Made the trip a couple of weeks ago - cab from airport to water taxi was $17.50US for all three of us. Water taxi one way was $15.00US each - (they take credit cards w/small fee or cash or travellers checks).
That said - we always take the flight back to BZE because we want to stay till the last possible minute. I believe Tropic was $55US per person.
I've never done the boat trip in less than 75 minutes, and I (and my luggage) have been soaked several times. To me it's a no brainer - fly. And have your camera handy - the views of the reef & islands can be spectacular. First time around try to be on the starboard coming to the island, and port leaving it.
First timers are biting off a big project trying to get the boat. They don't run all the time, they don't take reservations, and you will be totally stuck if you are late and make mistakes about how to do it.