Two things:

Accurate seat height. You should consider a bike fit from a reputable dealer/fitter. If you're riding a MTB or hybrid bike it shouldn't be as involved as a road bike fit.

Exact foot placement. This will involve adopting clipless pedals, a properly fitting shoe and probably cleat wedges or orthotic footbed. Wedges have eliminated knee issues for me on my road bike by ensuring leg/knee alignment. Mountainbike type pedals/cleats are a little more problematic, but can be addressed. A good LBS should be able to measure the degree of cleat alignment required and check your knee action. This should be part of a good bike fit session. In fact it should start from there.

Sneakers and platform pedals will not be able to provide the degree of accuracy of placement and consistency your knees require for comfort.