Assuming everything else is equal (both are equally powerful and influential and are pursuing equally vile goals with equally bad consequences, etc.), I'd go after the CE creature first.
My answer is premised on the assumption that in the D&D universe, Good and Evil, Law and Chaos are cosmic forces, and that a CE creature somehow adds to the power of Chaos as well as Evil: perhaps, by its example or its actions, more people are encouraged to ignore the law, or the society's accepted codes of behavior, or fail to honor the country's authorities and institutions.
If I was a paladin and working not just for the eventual triumph of Good, but Lawful Good, Chaotic Evil presents a dual problem.