MTA runs express trains. They don't get up to 100mph, but they skip many local stops along the way. Raising their speed to 100mph would likely not meaningfully increase transit time - you'd maybe shave off a few minutes.
It's definitely under capacity by that metric.
https://www.wnyc.org/story/subway-ridership-hits-65-year-hig...
The only issue is that then it arguably had a much larger tax base than it does now to fund it.
I mean when were these built, a 100 years ago? Surely there's room for improvement.
"The Trains Are Slower Because They Slowed the Trains Down"
https://www.villagevoice.com/the-trains-are-slower-because-t...
Similarly there's a top speed of 79mph on the rest of the country on most passenger rail since the Naperville Train Disaster of 1946
Because building a subway in New York City costs $4 billion per mile.