Most gearboxes are speed reducers- high-speed, low-torque is input in order to get have a lower-speed, higher-torque output. When this is the case, the pinion is the gear at the input. It is typically the smallest gear in the geartrain (because it handles the least amount of torque). If the literature you are using refers to a "pinion shaft", I would assume that this means that the gear teeth (the pinion teeth) are cut directly into a shaft which is then mounted to the gear case (as opposed to the gear being a separate item which is fastened to a shaft).