Very difficult, as both of them are truely legendary and have logged thousands of story arcs. As various writers depict their power sets differently, it can be hard to remember just exactly who we are dealing with here. Plenty of times Thor is just the guy flying around in stripey 80s spandex, taking orders from Captain America, and occasionally getting owned by chemistro. But when he truly unleashes the full extent of his power he is a god. Diana, admittedly a very powerful character, and a founding member of the JLA to boot, is in the end someone who has just been given a few gifts from the gods. Wonder Woman at the top of her game < Thor, God of Thunder and wielder of the Odinforce.
Of course, she would certainly put a good-sized dent in his chisled blond mug before going down.
Freedumbring 