Mass transit incubators
I’m not sure of the mass transit explanation. I work in the SF Bay Area where a lot of people use BART to get to work. Although there was an early outbreak in Santa Clara County, BART doesn’t go there. And SF has been very lightly affected by the virus.
I think it’s more that—to compare the two cities—SF had a much earlier “lockdown” than NYC. The earliest in the nation. As far as a comparison of deaths, SF also has a very small black population (to compare to NYC), low obesity rates, less diabetes etc.