Carbonfiberboy is probably right, because that is a common problem of cyclists when taking on new hills or hills for the first time. The first year I started riding my knee pain came from a tight IT band (which foam rolling greatly improved) and weak VMOs. The patellar pain (from patellofemoral pain syndrome since there was no cartilage damage) was diagnosed by an ortho doc. His recommendation was to decrease riding and mix in other endurance exercise. I did not like this answer so I sought out ways to fix the problem. The pain was fixed by:

1) taking a week off the hills with rest, foam rolling and ibuprofen
2) taping the knee with kinesio tape to encourage the knee to track correctly until I could strengthen my VMO. See https://www.youtube.com/watch?v=PqaP...ature=youtu.be for taping technique. There are 2 techniques in the video, the second technique starting at 3:30 worked best for me.
3) strengthening my VMO using this technique (https://www.youtube.com/watch?v=S5BDi8Oj5eM) and doing lunges

Now I have no pain and I do not need to use kinesio tape. The bike fitting is a good idea, but if the pain persists after the ortho analysis and fitting, then it is probably a weak muscle issue.