The best controller is whatever works best for you. Controllers are and always will be personal preference.

Generally, runners prefer to use the Gamecube controller to better realize and optimize their mashing.

@JackRG Are you playing on Wii U or Game Boy Player? Cause you can't use a GameCube controller on a Wii U.

@JackRG Yes, you can use a GameCube controller on Wii U through homebrew and it's absolutely allowed for runs on the leaderboard!

Apologies, I didn't consider homebrew