It's easier to get there by air. Last time I was there I went to CC twice; first time when we first got there (by ferry) and then we flew back from Flores, Guatemala and took the flight to CC (purely to save time and sneak in a dive that day). If this is your first time, you would be robbing yourself of a very unique experience if you flew. Take the ferry. You get to see downtown Belize City, you get to see all of the beautiful cayes on the way, and you will have a neat experience. Not to mention the fact that on the trip form the airport to the ferry terminal you get to pass the Belikin brewery, which is where the real magic happens in Belize. That's worth the ferry ride alone. 
