"Can you replace the plastic windows?" As far as I know there aren't any replacement pieces you can get to do this.
My suggestion would be to leave the window in the master cylinder and try to use some RTV sealant covering the entire inside of the window and part of the surrounding area. You will have to make sure the master cylinder is completely clean and free of any brake fluid! If you do not do this the RTV will not seal and it will leak again!
You will have to search around to find a RTV sealant that will hold up to brake fluid.
