Hi Aimee - this is such a common issue with runners, I devoted an entire chapter in my book on how to strength this area and help activate the stabilizing muscles.
If you are not into get the book, one great exercise to attack this is a one leg squat. They key here is to be sure to keep the NON-squating leg out in front of you while performing the squat with the other leg.
A good compliment to this would be to do one leg box step ups.
Do all of this barefoot to help activate the feet - all strength and stability starts at the feet.
Then while running, be sure to focus on good foot strike placement, again you help utilize your feet, which stabilizes the knee, and activated the hips/glute medius.
Hope this helps.