Surfer was more powerful, creating massive holes in the Earth that iirc went all the way to the core, driving Galactus away with a blast that looked like it would've obliterated Earth, matter manipulation etc etc. His only weakness was his board but if Thor were to knock him off, he could just recall it.
Thor might be stronger (I don't recall any Surfer strength feats), and Mjolnir is always a threat but I think that Surfer would've been too much for him alone.