Short answer is yes, it's absolutely too much hassle. Two things: last Metro North is 1 am or something, and then doesn't start back up for another few hours. If you budget about 3.5 hours, you may need to take a train the night before anyway to even make your flight. Second, depending on how early your flight is, even if you take Metro North to Grand Central and then walk from there to Penn (15 minutes), the AirTrain to EWR doesn't even run very early in the morning, which would mean you'd need to take an NJ transit train to Newark Penn and then an Uber or bus to EWR (10 minute Uber, 20 minute bus). Source: like an idiot, I booked a 7 AM flight out of EWR—had to leave at 10:30 PM the night before and didn't even get to the airport until about 4:30. It was a nightmare.