You can hope for an irop.

A couple years ago I was flying DL PHL-JFK-SEA. I was on a southbound train to Philly, still north of Trenton, when I decided to pull up flight status. My PHL-JFK was delayed to the point that I would miss my connection. I called DL, they saw the irop, I told them I could find my own way to JFK, they deleted the first flight, I got off the train at Trenton, picked up a northbound train, and still made my flight at JFK.

With EWR and a tight connection this would be even easier, I suppose. But you would have to get a CO agent to delete the PHL-EWR flight from the reservation before you miss it.