Since it's a chronic condition and the doctors haven't been able to tell you anything useful, you can't really spend years staying off of it. What about swimming? You can get a lot of exercise swimming without putting a lot of strain on your legs.
About cycling, are you riding every day and then one day you go for a longer ride and the pain starts? Or do you decide one day randomly to go for a long ride, and the next day your knee is killing you? Most of us are sore when we haven't been on the bike in a long time. It sounds like maybe working up to a longer distance very gradually would let your body get used to the exercise without the soreness...assuming that the seat height is right and that you're shifting gears efficiently to minimize strain on your knees.