I injured my knee a couple years ago and the best cardio for me was low impact kickboxing and modifying floor aerobics to low impact. But I also went through physical therapy and they basically had me doing stuff I could do at home with my DVDs (mostly strengthening the quads and hamstrings). The ironic thing was my doctor told me not to do lunges or squats and the PT had me doing just those! But I'm sure it depends on the injury/pain you are having.
One thing you might want to consider if you haven't already, is getting your shoes fitted properly. I didn't realize my feet were pronating, and I needed orthotics and better fitting shoes. Because of the pronation my knees were not aligned properly and it was adding to my pain. Also, stretching the IT band was a huge help for the pain.
My doctor suggested swimming and the elliptical for cardio, but both seemed to bother me.
Again, I'm sure it depends on the injury/pain.
Good Luck! Knee pain is no fun!
Julie