Yeah, the Bay Area has too many rich outer areas to make any sense of it. The one about New York from about a month ago is a lot more clear - rich center, poor periphery. http://www.newyorker.com/sandbox/business/subway.html
In both NY and SF, if you keep going further out (beyond the base mass transit system) incomes start to rise again. There's basically the rich central city, the poorer surrounding "urban" neighborhoods, and then the rich suburbs. Chicago too.
I guess that was the point. Both places have inequality, but the Bay Area is wacky, and not so evenly covered with mass transit. And the mass transit that exists is fragmented between different agencies.