I think eveyone would agree that Wonder Woman is much more popular than Thor.
Wonder Woman may be more widely recognizable than Thor, but I would argue about her "popularity". Her current well-deserved success in the Nu52 is sadly the exception rather than the rule. Historically the WW comic has always struggled to find readers, as her frequent re-inventions can attest. Hardly the sign of a historically "popular" character.
Thor, on the other hand, has largely been a consistently steady, if not always spectacular, selling book.