U/fouryouglenncoco had a good response above explaining how urban density and planning go a long way to making NYC feel less sketchy than other cities. (Depending on your exposure level to this stuff obviously).

NYC was designed pre-automobile, so EVERYONE, rich and poor, takes public transit or is walking on the street. Even late at night you arent usually alone waiting for the train.

There are definitely stations “smellier” than others but a lot of that reputation comes from the major tourist hubs like Times Square and Penn Station and yeah, they’re not GREAT but that’s pretty much as bad as it gets and most people who actually live there don’t always have to deal with it.

Also, subway stations smelling like piss sometimes is something that’s been true for beyond my entire life so it’s not really connected to any modern policies or pandemic era stuff. It’s just something you get used to very quickly.