Unfortunately, we can't tell you the reason for your knee pain. It may be physical, it may be equipment (poor fitting/worn out shoes, etc) or something else. I would recommend getting with a trainer and/or physical therapist to help figure out the cause.
There are many exercises you can do that don't put that kind of stress on the knee, however. Swimming is one, that is almost entirely non weight bearing, and is an excellent cardio option. Another may be a properly fitted bike. While that involves knee movement, it's nowhere near as weight bearing as walking/running.
Ergonomic rowers or actual sculls, all the weight machines and some HIIT exercises are all options as well. And, as you get stronger, you may find that your knee pain lessens too. If you do consult with a physical trainer, make sure to ask them for a list of good exercises to work on weight.
Finally, weight lifting is one of the best methods to transform weight. Don't be so focused on the scale, as the mirror. Muscle weighs more than fat, so initially you may lose a lot of weight (Depending on your start point), and then gain some back as you add muscle. But, muscle burns more calories to maintain, so more muscle = more calorie loss.