Eric Alexander and Peguy luyindula were both on target as New York got the better of the Eastern Conference leaders at Gillette Stadium before the FIFA World Cup break.
The win ended New York's drought, having lost to the Chicago Fire (5-4), Toronto (2-0), Portland Timbers (2-1) and drawn with Sporting KC (1-1) since defeating Dallas (1-0) at the start of May.
"I'm extremely proud of my guys," coach Mike Petke said.
"I told them before the game that there were going to be periods tonight that were not going to be pretty and that I'm absolutely fine with that as long as they put the work in and play for each other.
"That's all I wanted, to be honest with you, at the end of the day. I was here the last time we won 10 years ago.
"I played in that game, so I am extremely proud of them tonight."
