I'm experiencing something similar right now in my left knee but I think mine is the hamstring tendon. This is a first for me. It occured right after my first Century ride this year. Like you, it only hurts when I'm pedaling and more noticeable on inclines. I'm not sure how to treat something like this. I just hope the answer isn't to stay off the bike.
report back on what the doctor tells you. I hope its nothing too serious.
Edit: I found this explanation on how to strengthen your problem muscle.
http://www.merck.com/mmhe/sec05/ch075/ch075f.html