I'm sure part of the problem is that subway workers in NYC are well-paid, but that's probably not all of it.
NYCT workers are well paid, but that is only an explanation for high operating expense, not obscene capital expenses.
Operating expense is really fairly well managed, albeit with unusually high wages. It is a small, small part of the subway’s problems.
Train conductor base pay is $23-30 an hour - the six-figure salaries that you read about are for people doing >40h/week, including night shift/holiday/on-call work.
I generally think that it's reasonable that people who do more work get paid more then people who do less work... Or that people doing the same work during hardship hours get paid more then people doing their 9-5.
[1] https://www.nytimes.com/2017/12/28/nyregion/new-york-subway-...
For those interested in analysis of subway construction costs, I highly recommend Alon Levy's work at Pedestrian Observations: https://pedestrianobservations.com/construction-costs/
[0]https://www.citylab.com/transportation/2018/01/why-its-so-ex...
Does not help that NYC is paying 5-10x that. Given that, the former comment is pretty much in line, even if slightly exaggerated.