Yes, I will agree that "barefoot" running is better on your knees than with standard running shoes- also running with proper form would be, but alas- almost no recreational runner will do either of these things, and it is especially hard to do so on typical running paths (such as, you know, roads).
Given the constraints of what we're given, biking is far better for your overall health than running.
I walked in to work this morning, during which time many runners passed me. None of the women--and most of them were women--were heel-strikers; from my past observations, few women are. And of the three men who passed close enough to see, all landed on the middle of the foot.
You don't need to run barefoot. Just tilt your foot forward and land on the ball rather than the heel. You can stick with regular running shoes and do this.
Given the constraints of what we're given, biking is far better for your overall health than running.