I think clipless is better in the long run for the knees and joints than toe clips, if for nothing else than with clipless once you get the proper positioning, your foot is held in the right place. With toe clips/straps, you have a much greater occurance of sliding around and getting out of the best position, which could bother the knees over time.
My 43 year old knees creak a bit sometimes, and I get the 'snap, crackle, & pop' going sometimes too, but that's how I've always been.
It's probably just the muscles and tendons settling back into place once you're riding again.
But if you're having knee pain, it's usually a sign of improper saddle position and height, and/or misadjusted cleats. Go back and check those.