I can't give you any specific exercise suggestions since I'm not able to evaluate you in person, nor do I know your medical history. And as it was already pointed out, it could be caused by something else along the kinetic chain and giving you specific exercises may aggravate it/make it worse.
We do have a limited mobility resource center though, that you might find some helpful ideas/tips in there: www.sparkpeople.com/resource/lifestyle_cen
Was your physical therapist dealing with this issue previously? Or were you seeing them for something else? If you were seeing them for the knee issue, then they should have given you some exercises that you could do at home that would be safe and ideal for the condition your knees are in.