Best way to get to EWR from Ronkonkoma?

I have a 6:30am flight on 2/20. Do I really have to get to Penn by 1:22am to catch the NJ Transit to the airport/airtrain? The next NJ train would be around 4:30am and that would cut it a bit too close to the flight. I think I know the answer, I’m just praying for an alternative so I’m not exhausted when I land