can i seriously suggest getting clipless pedals...FROGS.
these are free floating and allow your knees to move naturally, as well as investing in a nice saddle and studying your seat positioning
you will use the proper full range legs muscles with pedals and become a better efficient spinner.
i have had knee pain my whole life due to large quads, small knee caps these two things as well as strengthing the whole leg has minimize the majority of my pain beside your typical getting older stuff.