Yeah, I spaced and forgot about the South Bay. The East Bay is decent, though. Well, the parts I have been to. Which I suppose are only the parts I found it convenient to reach by public transit, so there's a whole lot of sampling bias going on.

When I lived in Boston, I found that there were almost zero situations where it made sense to take transit rather than biking (especially anywhere in the vicinity of the green line!) unless there was a lot of snow, but in SF/Oakland/Berkeley I end up using transit several times a month even ignoring cross-bay trips. This is the source of my gut feeling that (my part of) the SFBA's transit is superior to Boston's.