I have bad knees too, but I'll spare you the details.

I've used both SPD and Speedplay pedals on my bike. I have slightly less pain with the Speedplay (Zero). I think this is because they have a bit of float. They're adjusted to have very little though.

Make sure if you get anything that they put you on the trainer and make sure the position is still correct and that the cleats are placed properly on the shoes.