Because they exist in different comic book continuities and no crossovers have pitted them against one another as of 2014, it's impossible to say for sure who would win in a fight. It is, however, possible to hypothesize based on their respective power levels.
Because these are fictional characters, it is up to the writers to decide who would actually triumph if they were to do battle. Although Thor is a literal Asgardian god armed with incredible strength and power, Superman is treated as even more powerful in most source material. In fact, although Thor's strength has limits defined by the Marvel writers, Superman has been described by DC Comic's writers as being as strong as he needs to be to fit the story. His powers have continually grown and expanded over the years. He would, in all likelihood, triumph over any foe the writers did not treat as equally limitless.