Squats aren't bad for your knees, typically it's how you squat that's bad for them. Shifting forward, lack of ankle mobility, knees going valgus. etc. My athletes and myself included always do a few sets of TKE's (Terminal Knee Extensions) before the first set and maybe the next 2-3 warm up sets, for the knees specifically. That movement helps warm up the VMO (vastus medialis oblique). It's the inner portion of your quadriceps muscle, which is basically the front of your thigh. The VMO is very important to train in the presence of any degeneration in your knee. If that's the case. There is a number of videos you can find on youtube for references.
Lift strong, and prosper.