While both share a fair amount of hax due to both being one with the Chaks Force, Knuckles has an edge in combat prowess that Aurora lacks. She was a scientist before ascending, and while she was a damn good one, it doesn't compensate for Knuckles' vastly superior knack for fighting and conflict. Not only that, but he has lol stats amp to quickly give him an AP advantage from when the battle starts.
Assuming Knuckles is one with the Chaos Force, he wins. While Aurora is the strongest of the Neo Walkers the encyclopedia says Knuckles became stronger than the Ancient Walkers when he became one with the force.