In short, the answer is no, there aren't really any good cardio exercises that are upper body only and don't involve the legs without the knees.
To understand, you need to know the structure of the knee, but suffice to say that there are tendons that go through the knee area and encapsulate the patella (kneecap) and there are ligaments that hold the knee together. (Tendons connect muscle to bone, ligaments connect bone to bone).
Pretty much any exercise (including swimming, unless you are doing strictly pull work) is going to bend the knee to some extent and involve the muscles of the upper leg, which will in turn place stress on the knee.
I would go to an orthopedist, and a physical therapist and figure out what is damaged and causing the pain, fix that, and then get back to working out regularly.