The float (the amount your heel/foot is allowed to rotate laterally when clipped in) might be important here. Many riders with knee probs opt for pedals that have lots of float (such as speedplays). Not sure how much float your pedals have (5 degrees?) or whether the float is adjustable. Check the manual. The amount of float probably matters much more where your knees are concerned than the size of the platform.

Another thing that might tell you whether it's a float/pedal issue is to go for an easy ride just in your tennis shoes. I think your platforms are big enough to allow you to do this safely. If your knee does not hurt after, it points toward your pedals/cleats as the culprit.

Good luck.