Can Sasuke's Amaterasu go through windows?
Yes, Amaterasu can pass through clear glass.

To quote the wiki


  Amaterasu produces black flames at the focal point of the user's vision.
  - chapter 390 page 3


The focal point of a users vision is located at the back of the on the retina as seen on the image below.

This means that whatever is being 'seen' by a user at that time, will be cast ablaze. Comparable to how you can either focus on something beyond a window, or if the window is dirty, the window it self.