Depends on where the GL vs. Magneto fight was. In a Junkyard or City, then it would be an interesting fight. A place with no magnetic materials and GL will win. The ability to create anything out of nothing means GL will always win unless Magneto can find a school bus.
Don't forget, Magneto's immoral. He has no problem bringing civilians in as part of his arsenal. If faced with a schoolbus full of kids or a commuter train being hurled at him, would GL take it out? I don't think so. Win goes to Magneto.