A few people used to live in the Amtrak tunnels on the Hudson River side of Manhattan. There was a documentary made about them [0]. They were evicted, and the tunnels fenced off, in the late 1990s.

I would be quite surprised if anyone was living in the subway tunnels. Compared to the Amtrak tunnels, they are much narrower. Additionally, people were living in the Amtrak tunnels during a time when the tunnels were unused or seldom used by train traffic. In contrast, subway tunnels see lots of traffic 24 hours a day.

[0] https://en.wikipedia.org/wiki/Dark_Days_(film)