GWB to RFK (via Harlem River Drive) to GCP to VWE. If you don't need to drive I'd suggest avoiding it (might seem longer on paper/time) but the reduction of stress to board the AirTran and zoom by traffic directly to your terminal is pleasant. Get to GWB Bus Center - take bus/shuttle to Manhattan and board A train downtown express to 34th St to LIRR to AirTran.

There is also a nice little delay getting from the VWE to LT parking at the Belt Pkwy is probably not enjoyable in the afternoon either. You can choose to stay on the Conduit.
I am an advocate for public transportation but have also been in traffic watching the clock go by and thinking crap I still have to get to LT and get on a shuttle and get to Terminal 8 to security without a good gauge when traffic will clear up. Live longer less stress and allow a train conductor to drive.