Hm. Two of my favorite characters. Lol. Lemme insert my opinions:
Durability - Surfer. Soaking several direct hits from 2 Galactus-level beings and still be strong enough to manipulate energies powerful enough to kill them both (and surviving that, too). Soaking an entire battle fleet's main guns focusfiring on his face w/o flinching, etc. I say Surfer edges out Thor in this category.
Single Target Hitting Power - Thor. Surfer has nothing on the type of opponents Thor has been able to hurt (unamped) when he's being serious. Smashing the Doom destroyer armor, piercing Exitar's armor, chasing Galactus away, etc.
Multiple Target Hitting Power (AoE attacks) - Surfer. He is the king of smashing large or several objects. Speedblitzing an alien battle fleet before they could even react, blowing up planets, creating black holes, etc. Surfer has this category aced.
Combat and Travel Speed - Surfer easily. Don't even need to explain this category.
Versatility - Surfer edges out Thor by just a bit. This is my opinion, they both have a TON of versatile feats
Here are more items I have opinions on, but will no longer post feats to back them up as I am tired and need to sleep. Lol.
Yes Surfer as done that. He was out matched physically against some monster then decided to take the fight to the astral plane where he owned it.
Thor's TP resistence is on and off. Sometimes you can have him kissing your boots other times he wills it off and slaps you in the face. But in Surfer's case I bet he can do it.