I'd go for Thor. Especially in a single contest. He's got the superior strength. Even if they're just tossing the weather around, the God of Thunder beats an X-Babe with weather-controlling abilities by lkjdflajfldkjflajllllion years of experience.
Granted, neither are deities per se - Storm was worshipped but is a mutant, Thor was worshipped but is an alien, but Thor's godhood remains unquestioned in the Marvel Universe. He's got his Nordic background, immortality, and everything else. Storm doesn't. In a contest of strengths, Thor's much stronger, his tech is wider. The only thing Storm can do is get Mjolnir away from him, but the thunder-god's knowledge of how a storm works isn't limited to Mjolnir, it's a part of his own mad strength. He'd K.O. Storm even without Mjolnir.