What pedals are you currently using? There are a couple things it could be: Your fore/aft saddle position may need to be tweaked; your cleat position may need to be tweaked; or you may need new pedals entirely. Have you had a bike fitting done? If you and your fitter have adjusted the first two things and you're still hurting, you probably need new pedals. "Float" in a pedal refers to amount you can "twist" before unclipping. That translates into how much freedom your knee has to move as you pedal. Large amounts of float (like that found on the Speedplay Light Action pedals--14 degrees) can be either a good or bad thing for knees. Definitely talk to a fitter.
I'm experiencing similar issues right now, I think. Good luck.