How is your soft tissue quality of your hip flexors and quads? How is the mobility of your hips? Glute activation up to par?
Do you have video of you squatting? I would be interested in seeing your technique during squats. Ideally, when somebody has chronic knee discomfort, I would recommend sticking to squat/lunge techniques that keeps a relatively vertical shin position, as to decrease the anterior shearing force on the knee.
Also, I would strongly cue the "hips first" and "hips back" approach during your squat. In terms of the front squat vs back squat, I would think that the front squat (which is much more quad dominant and produces more anterior searing force) would aggravate the knees more than the back squat, but that is all depending on your technique, etc.