By comparison, Crossrail in the UK cost a similar amount with a truly massive amount of new track, new tunnels and new stations. London is a reasonable comparison to NYC. London may even be worse given the age of the cities and the whole thing being full of ruins going back to Roman Britain.
This article mentions layers of consultants. Honestly, I think we'd be better off if the government was never allowed to spend another dollar on McKinsey, Bain, BCG, etc. They're just an exercise in wealth extraction from the government, providing negative value.