We live in Central NJ, looking for options to get her home, or at least within a 2 hour drive. Flights are a little too costly.
The Amtrak Vermonter runs once a day. It's a long ride and I don't know if it's less expensive than flying. There is also a Greyhound bus. Also, if she can get a ride an hour and a half south to Rutland, there's a different once a day Amtrak train (Ethan Allen Express) that is a somewhat shorter ride. But she can probably find fellow students with whom she could share a ride home.
Keep your eye on JetBlue as they often run sales on flights between Burlington and JFK.
When I went to UVM eons ago (ha) there was a "ride board" somewhere on campus where people could post notes looking for rides. There may still be something similar?
Google Maps suggests Megabus or Greyhound to Boston and then the Northeast Regional Amtrak train to Newark Penn Station.
It also suggests a somewhat convoluted, but shorter route ... using the local buses, get to the Burlington Airport; take a Boston-bound greyhound bus just three stops and meet Dartmouth Coach at the Hopkins Center and ride it to NYCity. From there, they suggest Greyhound to Penn Station.Edited: 9:34 am, September 26, 2017