There are three NY Waterway ferry terminals but for the most frequent service to Weehawken (Port Imperial and Lincoln Harbor) use the Midtown/39th St. terminal: take Airtrain to Jamaica Station and then take the E subway to 42nd St. Look for the red/white/blue free NY Waterway shuttle bus which runs along 42nd St. See www.nywaterway.com for info.
There are three NY Waterway