Lavan:
I used a PIR sensor module for the motion detection for a security light and fixed everything in a small transparent plastic box (PIR sensor module also inside the box). It is working fine without any issues. Whenever there is a motion it switches on the light. So I believe it works for your case as well with out any issues from behind the clear glass. Just give a try!!
Plastic an glass are very different categories of materials, and even different types within those categories can have very different optical or other physical properties. Furthermore, just because something is transparent to one set of electro-magnetic (EM) wavelengths doesn't mean it will be for another, even if the two sets are close to each other on the EM spectrum. Based on my own experience with IR sensors, in the mid-to-long infrared wavelengths (which is what PIR uses) window glass doesn't act like much of a window. There are of course types of glass that would be transparent to these wavelengths, but most aren't the type you'd get at your local hardware, art supply, or hobby store. Instead, you'd have to start with organizations that sell laboratory grade glassware and/or specialty optics.