Glass or poly-carbonate, most dyed through filters use an organic dye, which is subject to fading. Glass is more scratch resistant, but has a higher index of refraction, so it benefits from an anti-reflection coating.
It is possible to make a dyed through all glass graduated filter, but not economical ($$$).
Lee does make a thin film neutral density glass filter, which does not use organic dyes. The main reason is to avoid vignetting on wide lenses, as the oblique ray paths will travel through significantly more glass, and with a dyed through filter, those ray-paths would see more attenuation. I have not seen a thin film graduated ND filter yet, but they are possible, the same manufacturing techniques are used to make Canon's R series apodized element on the 85mm lens.