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.
New York, who leapfrogged Columbus Crew and Houston Dynamo into fifth position in the East, also claimed their first victory in New England since 2002, despite being without key duo Tim Cahill and Thierry Henry.
"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."
Meanwhile, the Los Angeles Galaxy and Western Conference cellar-dwellers Chivas USA played out a 1-1 draw in their derby clash at StubHub Center.
Erick Torres opened the scoring for Chivas in the 20th minute before the home side responded through Gyasi Zardes 15 minutes later in Los Angeles.
The Galaxy are seventh in the West after back-to-back draws, six points ahead of strugglers Chivas, who remain at the foot of the table.
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