Superman is unquestionably the more popular of the two. There is no arguing this. Stiltman might be correct when he talks about Goku being more popular relative to time(I don't know the state of the comic book industry between the late 30's and 60's but it seems to me most books would try to create characters that distinguish themselves from Supes, rather than trying to appear like him) but that has to do with something Toriyama could not predict.
Clark's popularity isn't really a surprise though. For starters the bare basics are so easy to understand one only read his name. "Superman". As in, the best man. Man taken to the next level. Son Goku is a name that only means something if you know Journey to the West.
There is so much more though. Superman was developed in an English(most widely spoken language) speaking country, Goku for an island nation that only spoke Japanese. Goku was written/drawn by one man for a little more than a decade with three different animated adaptions. Superman has been published regularly since his creation, has several cartoons/cartoon related materials related to him get tossed out there, and has several movies produced by Hollywood(the most important name in the film industry). When Superman "died" he had four books going on at once, something flat out impossible for Goku. Perhaps most importantly, Goku is not part of an extended universe that includes all of mangadom. Most mangaka have been influenced by Goku/DB and all have heard of Toriyama but their worlds are theirs. Naruto is not forced to share the spotlight with him. While Superman is considered not only the heart and soul of DC but the purest example of a Super hero comics have to offer. Goku really isn't even the most popular character to come from Japan. That honor probably goes to Godzilla. To be fair though Superman isn't likely as well known as Mickey Mouse but ya get the point.
No what is impressive here is that Goku is as popular as he is. By all rights he really shouldn't be. He should have just gone away. But Goku has a significant advantage as well. He was conceptualized and later made public in the West during the raise of the internet. The themes inherent to Goku's character also probably have better appeal to those of us today. Superman is often seen as a boy scout and whether or not that image is true that image has stuck. There are many facets of his character that make him a far more interesting character to explore than Goku, and many authors have, but fact is DC needs Superman to be THE Hero. Goku has been allowed more growth. He gets a kid, he gets a permanent wife, and he eventually gets to become a god for real. With comics you're never quite sure what will stick and what will not. With Goku it is clear. He's gone from being a child who knew nothing about the world to a martial artist fighting his master for the right to be called strongest under the heavens to fighting gods himself. All the while the theme of training oneself, mastering ones own abilities, and becoming the best you can be are placed in the background. These are the reasons Goku has struck a chord with so many, along with a few other details.
Now does this make him more popular than Superman? Well it depends on what you mean. In sheer terms of how many people know about them, Superman takes the cake. But the real important question regarding Superman isn't whether people know him or not. The question should be how many people actually care about him existing. I personally love the idea of Superman and examining his effects as cultural cornerstone. I even love the stories one can get from him. But have I read a single comic or gone out of my way to watch films about him? Not really. I don't think I'm alone in this either. The vast majority of the internet, for better or for worse, prefers Batman by a wide margin due to the latter's incredible good luck when it came to quality adaptations. Man of Steel made tons of money but right now there is no doubt the super hero film firmly belongs to Marvel. Between Marvel and Batman, Superman's prominence in the eyes of the popular audience outside of comics is dwindling.
Whereas Goku...well like I said he really ought to have died by this point. His manga ended in 95, his anime hadn't been on television in quite a while, and GT was widely disliked. DB Evolution should honestly have just killed the worth of the IP for good but it didn't. But the series left such a massive impact that it has been brought back several times and is now experiencing a rebirth in the films and Super.
A good example of the state of things is to look at the box office. RoF was advertised as "Freeza is back and the gang has to stop him from destroying the Earth!" It is a shameless cash grab in every sense of the word. Bringing back the series most popular bad guy just so Goku could defeat him once again. It even ends with a psuedo deus ex machina. The box office results might even speak for themselves. RoF's overall lifetime gross is only $61,768,190. Compared to Man of Steel($668,045,518) the winner of the popularity contest should be obvious. However that ignores several key factors at play. MoS was published by Warner Bros(big name) while RoF went through Funimation Films(utterly unknown to most audiences). MoS had Snyder and Nolan whereas RoF had...well no one anyone would have heard about working on it. Most damning, MoS was released to 4207 theaters for 22 weeks. RoF was only in theaters, at least here in the states, for 2 weeks and in under a thousand theaters. For an anime movie, RoF did fantastic and is rated more highly on Rotten Tomatoes than MoS. Now compare MoS to Dark Knight Rises($1,084,939,099). That is a significant gap for two films with similar amounts of distribution. Superman is unquestionably better known than Batman but his films lose out in every way. And the Guardians of the Galaxy are definitely not as well known as Goku, never mind Superman, and their film launched them into the forefront of comic book heroes with $774,176,600. That by all rights should be impossible.
Not that any of this affects a vs thread. I just wanted to throw my ideas on the subject out there. It doesn't matter to me who is more popular.