How can my window shake while im running?

In this case, I think that moving the camera around would work better than rotation. In the simplest case, I'd make the camera a child of a 'shaker' object, that randomly moves around whenever the screenshake is active. You might want to include some damping, but in the simplest form, it goes like this:

 transform.localPosition = Random.insideUnitSphere * shakePower;

where shakePower is a float between 0 and infinity.

To damp it, have the position interpolate between points ever few tenths of a second.

 currentShakeTime += Time.deltaTime * shakeSpeed;
 transform.localPosition = Vector3.Lerp(previousPos, nextPos, currentShakeTime);

 if(currentShakeTime >= 1)
 {
     previousPos = nextPos;
     nextPos = Random.insideUnitSphere * shakePower;
     currentShakeTime = 0;
 }