Public transit is expensive.

Boston's T was doing quite horribly as recently as last year. It still cost billions upon billions of dollars to function even at that unimpressive level. It needed even more funding. It got a partial infusion of funding to catch up on decades of lapsed maintenance — and new leadership, which was absolutely critical — and the system is doing far better right now, with further improvements planned through 2027 if the funding can be maintained to enable those improvements (not certain).

NYC's subway needs are far greater than Boston's and will consequently cost far more too. I wouldn't be shocked if the MTA could seriously benefit from a change in leadership, but often insufficient funding is the core issue facing these kinds of systems.