@thetrolldance: Well there seems to be no easy answer. It is partially, and partially it is not. The thunder and storm he can call from the skies is weather manipulation, redirecting what's there basically. Magic by definition is either creating something out of nothing or being something that can't be explained. The lightning part of his lightning that IS magic however, comes from his hammer or his hands, I'll quote a part from his page here:
"Thor has a strong affinity with the forces of weather and acting as a conduct can channel Mjolnir's powers through himself allowing him to summon lighting from his hands."
Though if It's a Superman vs Thor argument, his "magical" lightning wouldn't be the top of what Thor has in his arsenal against Supes.