ATC is severely understaffed nationwide and it's particularly bad in the New York area even without a government shutdown. It's a difficult, stressful job and was already even harder because mandatory overtime has been the norm for quite a while. So it's not surprising that when you stop paying people... some of them will start finding reasons they can't make it to work.
This has been a known problem for a very long time and Congress has continuously refused to do anything about it.
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