I have a cranky right knee that I also had years ago playing tennis. It is probably best if you seek professional help. It may be that just a professional bike fit is all you need. It will be helpful if you pay close attention to your pedaling movement. In my case, I noticed the knee would flop to the inside, occasional brushing the top tube. I added a 1 degree shim under the cleat and built up the arch support in the right shoe, all of which keeps the knee moving straight up and down with little inward flop. I further do knee exercises to strengthen the knees.

My knee problem is due to some trauma suffered in earlier years but I seem to have dealt with it successfully. If your knee does not have serious structural problems, it may be a bike fitter will help you. This is why I suggest you pay close attention to how you pedal. To paraphrase that great American philosopher, Yogi Berra, you can tell a lot by observing. I watch cyclists on the bike path here with legs and knees flying every which way and marvel those knees don't disintegrate before my eyes.