Both of them are practically the same kind of incarnation, though I'd imagine SS4 Goku going from getting his strongest attack tanked to tooling Yi Xing Long is enough to give him some edge in the beyond natural limits category.
I'm going to have to go with Ultimate Goku. I like to think Old Kaioshin's ritual is the absolute pinnacle of power (at least, at the time) for anyone, or that it trumps any other kind of power up.