I am a regular rider, and there are very few facts and a lot of anecdotes thrown out here. I do not think the subway is falling apart -- there are always problems, but in general, I see incremental improvement; we see more newer cars as the old ones phase out, and we're getting train arrival information throughout the system. Crowding is a problem as demographics shift, but trains run frequently during rush hours. From what I hear, the L is the worst for overcrowding, but most of the other lines handle the capacity fine.
The problems that we continually have with broken switches and rerouted trains and shutdowns, etc., don't seem to have gotten worse, but are just a perennial problem. I can totally see why it has been hard to fund it, because despite articles like this trying to stir up things, things really don't seem to be getting worse. That's not to say things are great -- you only have to ride another subway pretty much anywhere to see what you're missing out on. But the NYT's attempt to paint the subway as being on the precipice of a disaster rings false and only serves to hurt the cause of improving the subway by creating an air of alarmism.