American media says parishioners cried and gasped as the news was read out at Sunday mass.
In total 55 new parishes will be created by the largest reorganisation of the diocese.
"I can well understand the frustration, the anger, the confusion of our people, and I apologize for it, because I am the agent of it," Cardinal Timothy Dolan said. "But this is about the future, this is about strength and renewal, and we will get through this."
Around 31 churches are expected to close completely while the rest will see a dramatic reduction in services.
The announcement wasn't a surprise to most as the number of priests in the diocese continues to fall.
Retirements outpace ordinations and attendance is declining.
In 2013 a study showed just 12% of New York's 2.8 million Catholics went to mass.
Some parishioners are promising to campaign against the decision.