That's a really tough call. I'm tempted to use the line "You're comparing apples and oranges" because it's two different titles you're comparing. If I had to choose which one I liked better it would be Walt Simonson's Thor. The title had really been floundering for a while until Simonson took over, and right from the start (that first cover with Beta Ray Bill) the book was off to the races. Byrne's run on Fantastic Four had more of a slow start to it.
Another part of my reasoning is the personalities of the two writers. Simonson is a very pleasant man with a good reputation for his dealings with others. Byrne, not so much. I've become less and less of a John Byrne fan as I've grown older and read about some of his shenanigans. Also, I like Byrne as an artist better than Byrne as a writer. To me, Byrne's greatest work will always be his collaborations with Chris Claremont on the X-Men. In Simonson's case he is equally adept at both writing and drawing.
Now if you were to ask me who draws a better Superman... John Byrne would win that one hands down.
The 2 best things John B gave to us was Gladiator and Galactus as the Third great power in Marvel, but think Uncle walt had better overall flavor!