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There are flights you can look into between the two airports.

You can take a taxi between the two but it may be expensive. it is a long distance and you cross states and therefore tolls. There should be no traffic at that time though.

You can also take the Airtrain to Jamaica station. Transfer to a LIRR train (long island rail road) to Penn Station. Transfer to the NJ transit train to Trenton that stops at the air port. Check train times though if possible because if you miss the last train out of Penn Station (around 2am) to Jersey the next train is not until after 5am in the morning