The NY MTA does an admirable job, the issue I take is pretending that they're perfect. New York is pretty well connected, sure, and I can't think of another city that runs a subway 24x7. Even Tokyo shifts to buses eventually.

  Trains go every 10-15 mins even some time past midnight. They go every 30 minutes at time like 3 am; so do some buses.

Right, but OP was going on about rail service (with some key facts wrong). Buses stuck because they get in traffic… well all Muni Metro routes operate in traffic for most of their length (and one operates entirely in mixed traffic).

Muni schedules Owl (1–5 AM) bus service every 30 minutes. They run some regular bus routes 24x7 (not-Owl), Owl buses along the light rail routes, as well as a couple mega Owl routes to make up for the local routes that don't run late night. Except for Treasure/Yerba Buena Island (and the uninhabited islands), you can get within about 1/4–1/2 mile of anywhere in San Francisco on Muni. Evening rail service is like every 20–30 minutes on each line which equates to 10–15 (or better) underground since five of the lines run along the same subway tracks.

  Compared to some other large cities around the world where I've been, NYC is pretty well connected, and Manhattan (all of it) is superbly connected.

Yeah, New York City is generally well connected if you take into account the bus service. But so is San Francisco. I'd argue that the outer lands are better connected than the outer boroughs, but SF is so much smaller geographically that's not a fair comparo.

And yea I've done the subway bus shuffle in Queens (both because of subway maintenance and because of the distance to the subway) in the middle of winter. It's doable but OP was going on about not needing buses in NY. I've also done the late night subway thing and caught an earful from some natives who were real unhappy about all the transferring they had to do.

It's not that NY transit is bad or that San Francisco transit is particularly good. The idea that public transit in San Francisco is uniquely bad and grimy is just frustratingly wrong. That said, BART really shit the bed today when someone walked into the transbay tube. The mind boggles.