It is not recommended to use Windex on granite countertops. Most commercially available cleansers are either acidic or alkaline, and Windex is alkaline. These products can either strip the sealer on the granite or etch the stone surface.
It is better to use either a store-bought, pH-neutral cleanser or a homemade one. A gallon of warm water mixed with 1 cup of vinegar makes a pH-balanced cleanser that also disinfects surfaces. If the smell of vinegar is bothersome, another homemade recipe to make a pH-neutral cleaner combines 1/4 cup of mild dish detergent mixed with 1 gallon of warm water.