If you are refering to the window facing the bed, you first need to know the window can break when you are doing this.
Get a can of silicon spray and a thin steel wire about 4 feet long. With your hands, pull outward on the rubber seal around the window and spray the heck out of it with the silicone so it is totally lubericated. Carefully place the steel wire between the seal and the frame. Using a sawing motion, work your way around the window using slight pressure to remove the glass as the wire works its way around.
I've done it several times, but it is still a pain. Be careful not to damage the truck, the glass, or the rubber molding with the steel cable you use. You can also use a nylon string. You will need the molding for the new glass.