Flying to JFK from Buffalo you will not have to deal with customs/immig. Airtrain/subway will cost $7.25; take Airtrain from your terminal to Jamaica Station and then E subway to 50th St. Transfer to the uptown C subway one stop to 59th St. The M57 or M31 bus runs on 57th St. and you can take these buses to West End Ave. which is a block from 12th Ave. The cruise terminal is at 55th St. and 12th Ave. Travel time from JFK is about 1-1/2 hours. Taxi will take you direct for a flat rate of $45+tolls+tip.
Flying to JFK from Buffalo