I have owned neither, however I do have an old Winchester Modell 55, take-down, which is mighty close (if not the same) as a 94, and it's a nice rifle. That said, and going purely by my grandfather's advice, ... he told me if I wanted to buy a lever gun and i was deciding between Marlin and Winchester that I should buy the Marlin. The only reasons he gave me were ...

1. great barrel for accuracy
2. stronger and better lock-up of the bolt
3. Smoother/tighter action on the lever.

I am not a smith, but pretty much took him at his word... however I have never researched it.

Everything else that was different, he said, was a matter of personal preference.

He always said that the Winchester was a good rifle, but that his preference was for the Marlin.
He used to fix all kinds, and he said there were far fewer issues with the Marlins that came in.