Conversely: tons of people here in Vancouver complain about our equivalent systems (the Skytrain, usually), whereas people I know who've visited from New York are blown away by how clean, fast, and efficient it is. Trains that come every 90 seconds, no garbage on the tracks, bright, open, airy stations (most are above ground on that line).
NYC is a model of public transit from the perspective of ubiquity, feasibility, and ridership, though, and that's pretty key.
We also visited the SF Bay Area, and it was confusing as hell. The BART? The Muni? The buses? The cable cars? Who uses what? How do we get around? I need different passes? Oh, the tap card works? What's even going on?
I found the BART was very reminiscent in a lot of ways to Montreal's Metro system, but the MUNI (we took the J line? I kept calling it the JUnit, to my wife's annoyance) and it was 'fine', but only because we were a few blocks away. It felt very… rustic. Unmaintained. The raising/lowering stairs thing was a neat solution though.
In short, NYC being better than SF isn't a high bar, but I think we should all be happy that we live in cities that have such transit systems at all. Many large cities in the US don't even have public transit systems that can get people anywhere with any efficiency.