You'll have no problem getting to the airport. Takes 10 - 15 minutes. Last time we were there (Sept. 03) the cost for 2 adults with 1 big bag and 2 carry ons was $16 total.
At the airport there's a dispatcher who writes up a ticket with your destination, no. of bags and give you one and the driver one. No doubt about the price that way. The dispatcher usually speaks english but most of the cabbies don't, or not much. I don't remember if it was the same dispatch system at the pier. I don't think so. I love sailing from San Juan - enjoy!