I commute into NYC from Queens and I would say less than two miles of that is actually in manhattan and before 7am there is usually more, um.... breathing room.

Coming home in rush hour I would believe I suck a lot of tailpipe. Sometimes fumes on the bridge are noticeable.

During the coldest days when I wore my neoprene skimask I thought I could notice the mesh filtering some exhaust, but I could have imagined that.

I'm thinking in my case, after losing significant weight, and improving my cardio, I'm better off than if I didn't bike commute, health wise.