Scrub the surface heavily with steel wool, getting as deep into crevices and corners as you can. Don't worry about the roughness of the steel wool; it won't change the look of your cover.
Use soap and water to wash the cover off. This is usually most convenient when you are washing the rest of the vehicle.
Scrub out cracks and crevices on the cover with a toothbrush soaked with a lime-cleaning agent. This will dig up rust and any other residue that has built up in the corners. It will also help to remove set-in stains that have formed on the metal.
Rinse the cover with water, and give it plenty of time to dry completely.
Apply a standard metal polish to the cover, using a microfiber rag. Work with small amounts of polish at a time to help keep the coat as even as possible. Try to begin by applying a small coat, and apply more coats as desired.
Once the polish has soaked and dried, gently rub down the cover with a leather shammy. This will bring out the best shine in the metal.