How bizarre. I'm still not clear what exactly hurts. Your knees? Your entire leg? Muscles, tendons, bones?

I have knee problems too. Basically I can't do anything that puts a lot of resistance on the knee when it is bent. I can cycle, but it has to be fairly low resistance (have you tried this?). I can do leg presses, but I can't allow my legs to go less than 90 degrees, or I'll get sharp pain in my knees. It was determined once (by x-ray) that I have too much tilt in knees.

As for non-leg exercise...there aren't many. My gym has an arm ergometer (basically a bike for your arms). And there's swimming, of course.