I knew this would be a very close battle and I didn't want to say Surfer, just because I am partial to him even though I like Thor quite a bit as well. So, what I thought to do is something my Dad and I use to do when I was a kid to determine something's value. We would add up all the points to see who came out on top. So, I consulted the Marvel.com. power grids for each character links below.
Now, using the official power rankings set by Marvel if all of the points are added up in each category you end up with 36 points for the Silver Surfer and 35 points for Thor. While fans rankings came in with 40 points for the Silver Surfer and 41 points for Thor. So, you can see a very close match up in both cases, but that in each case the fans felt these characters are more powerful then what Marvel perceives them to be. In the end though I felt the correct rankings were the ones put out by Marvel as they are official.
Now with that said one could argue, by looking at these rankings that the Silver Surfer won the overall rankings only due to superior intelligence, where as Thor had him beat in Fighting Skills which is perhaps more important to a battle, but I believe it is all relevant and that the extra intelligence would tell Surfer that he could not beat Thor in a hand to hand battle and that he would have to battle him from a distance, and that this would give him the upper hand in the battle, and given the Surfer's speed over Thor that shouldn't be a problem. I see it as he keeps Thor away from him and just keeps hammering him with the Power Cosmic. So, I voted Surfer.