If you are in San Juan before noon, you can make it to Fajardo by using the public car system ("carros públicos"). Give yourself at least 4 hours to make sure you get to Fajardo on time. First, take the bus via Old San Juan
($1.50) or a taxi from the airport to the town of Rio Piedras (about $20), ask the driver to take you to the Rio Piedras central public car station and to leave you at the stop for the cars going to Fajardo "playa" (beach). These publicos will take you directly to the Fajardo ferry boats or to the Fajardo airport.
If the 'Fajardo Playa' vans are already gone, you can still take the cars on the regular Fajardo plaza route. Unless the driver agrees to take you all the way to the airport or port (they are not supposed to do it) you will end at the Fajardo plaza where you will take another public car to the airport or ferries. The whole trip in public car costs less than $6 per person.
Take a Taxi to Fajardo.
The P.R. Tourism office in San Juan 1-800-866-5829 told me (on 3/11/2003) that a taxi from the airport to Fajardo will charge you on the meter. They can not give me an exact dollar amount but estimate it will be about $65. The maximum # of people in a taxi is 5. When you get to the airport at San Juan, check with Ground Transportation Dispatchers (or you may call their office at (787) 253-5491).
Rent a one way car.
If your party is bigger than 2 people or you have a lot of luggage, you can save some money by renting a one way car at the international airport and driving to Fajardo. Leaseway (787) 791-5900 will rent you a one way car from $32 to $60 (minivan), plus insurance $10-$12, and a drop charge of $25, for a total of about $67-97. They can pick you up at the San Juan International Airport, you drive to their Fajardo branch (787) 806-5000, and they take you to the Fajardo Airport or port. Or you can do this in reverse. L&M Car rental (787) 860-6868 has similar service available. Some seasoned travelers recommend flying to Culebra and on the way back driving and stopping at El Yunque, the only tropical forest in the U.S. National Forest System.