Knee pain, as multiple people have mentioned, could have a variety of sources. I would suggest visiting your doctor and seeing if he or she thinks that Physical Therapy might be a good idea. From personal experience, PT did not work for me. I have found that running is not tolerable, on a long-term basis. On the other hand I have found upright or recumbent cycling, incline treadmill walking, hiking, or elliptical machines to be very tolerable.
Unfortunately, we don’t have it all figured when it comes to knee pain. While Physical Therapy can be great and may work well for you, I’ve also seen it fail to decrease pain in others. I hope that you find something that works for you!