Ok, to get to Newark, you would want to take Airtrain to Howard Beach, transfer there for the A going into Manhattan, get of at Broadway-Nassau Street in Manhattan, make sure you actually follow the exit signs to Fulton Street and make a left on Fulton, walk past Nassau and Broadway, and you will come to Ground Zero(unfortuantely).
Then take the PATH to Newark Penn Station
HOPE THAT HELPS
JFK