I have had knee problems for years from cycling and so far, I have managed to keep on riding in relative comfort. So have hope!
It's not possible to diagnose a knee problem without actually seeing you. My stock answer to this kind of question is to find someone who deeply understands bicycle biomechanics, and ask them to watch you ride. Their recommendations can come in at least four flavours:
1. Substitute bike components. The frame is too small or too large, cranks or stem too long or short, etc. Hope that the problem isn't the frame!
2. Modify bike geometry. The seat, cleats, handlebars, etc. are not positioned correctly. It takes an experienced eye to spot subtle problems. I had knee problems once because a cleat was out of alignment by about a quarter-inch!
3. Modify your pedaling technique. You may not be pedaling correctly. For example, some riders's knees describe a large figure-8 as they pedal, and this torquing motion puts tremendous stress on the knees. This was my bad habit for many years (for my right leg only) and I did not even realize it until it was pointed out to me. It took me a whole season to unlearn this habit: I had to learn to apply force straight down into the pedal, and resist the "natural" tendency of allowing my knee to drift horizontally/outward during the rest phase.
4. Stretching, strengthening, icing, heating, etc. Your problem may stem from a muscular imbalance, a slight difference in leg length, or a subtle skeletal misalignment. Knee problems sometimes respond to doing the right exercises in the right way. It is important to do the exercises properly. A sports medicine doctor told me that my quad strengthening exercise was likely making my problem worse! He showed me a better exercise, which I still use. Note that you may be doing exercises for several weeks or months before you get results. It is not a quick fix. For me, I do exercises for two to three months to restore my knees to their proper shape after an incident. (This past winter, I started jogging again, and that caused a knee flair up.)