Walk down to 50th St. and 12th Ave. from the cruise terminal and take the M50 bus (runs along 50th St.) to the C/E subway station at 8th Ave. Take the Queens-bound E subway to Sutphin Blvd/JFK and transfer to the Airtrain to your terminal. Fare for bus is $2.25, same for subway, Airtrain is $5. If you don't have a Metrocard the bus will only accept coins, no bills, so get a Metrocard to pay for all...bus, subway, Airtrain.
Walk down to 50th St. and