Well the last thing I would do is try them on the smith machine, because that will place you in a completely unnatural position with the bar in a fixed plane of motion (unlike actual squatting) and will be even worse for your knees!
You say you know your form is good, but everybody can benefit from rethinking their form now and again. For example I asked you what style of squat you had, and you just gave a very vague response along the lines of that you squat 'to 90 degrees'. This suggests that you don't really know what I'm talking about when I asked you about your bar position: When you squat the bar will always be in line with your feet, if it isn't then you will either fall backwards or forwards. Using a high bar position therefore means that in order for the bar to stay in line with your feet your back must be pretty much vertical. This takes virtually all posterior chain activation out of your squat and transfers much more of the stress to your quads and directly onto your knees.
If you use a low bar position, however, in order for the bar to stay in line with your feet you are forced to lean forward more, transferring much of the movement to your hips and posterior chain. If you're doing it correctly, you are not just sitting down into a squat position and standing up again, you are sitting BACK as well as down.
That's not to say low-bar squatting is categorically safer on your knees, because olympic weightlifters use the high bar style as it mimics their competition lifts more closely, as well as front squats etc, and a lot of their knees seem to be fine. But bear in mind their training will generally use higher frequency but a lot lower load, they will not be squatting near their max all that often. If you are squatting to failure regularly (ie. once a week or more) then I definitely think low-bar squatting is easier on the knees.
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