My sister lives in NYC and we visit each other regularly.

Flying is awesome and it’s a 35 minute flight. JetBlue & American to JFK and Delta to LGA http://flyorh.com/

There’s also Peter Pan bus which goes direct between Union Station and Port Authority and is about 3.5 hours. One bus a day but it rally has always worked great and been on time. Definitely not as painful as NYC-BOS buses. https://peterpanbus.com/

There is also OurBus which is newer so I haven’t tried them yet: https://www.ourbus.com/

The train is not really a decent option unless you have an easy way to get down to Providence. (There is shockingly no bus from Worcester to Providence). Going backwards to Boston is silly.