This exact topic just came up in a conversation I had today about some friends moving to SF from Seattle. I told them they better check out the Human Wasteland map [1] when choosing where they want to live. Depending on their desired poop contact level, they may want to choose neighborhoods selectively.
The good news, it appears most of the human filth concentrates into a relatively isolated part of the city.
The bad news, this appears to actually be something you have to care about.
(I would never call any of the big East Coast cities "nice and clean", but at least worrying about wading through human feces is not something anywhere near the top of my list)
(also for the record, I found L.A. far more filthy on average than SF, just less poop everywhere)