In their 40+ year history as a console maker, Nintendo has created a ton of different controllers; which do you think is the best so far, and why?

I've never used it but I imagine the Switch Pro and the Switch 2 Pro controller.

People tend to be nostalgic for old controllers but in general they've just gotten better for all manufacturers.

Joy Con 2 or Switch Pro 2 depending on the day

Pro controller by far. Though mainly because it is nearly identical to the Xbox controller, which I use the most. 

While I like the Switch Pro controllers. They're just too prone to drift For them to be in my top 3.

1. The Wii U gamepad. While it wasn't the best when used as a standard controller for standard games. Any time a game was made that really took advantage of its features. It was just amazing that nothings really come close to it since. I was playing ZombiU recently and it still holds up really well. And a lot of that is because of the use of the gamepad.
2. The gamecube controller. Almost every game has a primary button that is used more then any other button. And having a contoller layout that embraces that is such a great way to play a lot of the time.
3. The snes controller. This to me is the best feeling controller when playing 2D games. It obviously isn't going to be much use playing 3D games but for 2D it's amazing.

Nintendo 64 because it forced Sony to design Dual Shock Controllers and made gaming more enjoyable.

SNES for classic 2D games. Just fits perfect for 2D games. Not used the Switch 2 pro controller but Switch pro controller is solid. It works with modern games without some nonsense of joystick placement like Wii U or awkward wires like Wii. Impossibly small D-Pad like Gamecube or a nub for a second analog stick like Gamecube. Switch Pro controller is a perfectly serviceable modern controller.

I swear, if you asked this question in ten years, the current winner would get one vote and whatever was the newest controller at that time would get like fifty haha.

Depends on the criteria.

Most Iconic: The NES controller. It's a classic emblem of retro gaming.

Most Influential: The SNES controller created the long-standard setup of shoulder buttons and a diamond-shaped arrangement of face buttons, while the N64 controller was the first to demonstrate the importance of an analog stick for 3D games.

Just a Damn Good Controller: The Switch Pro controller feels right (offset sticks 4 Life), has a long battery life, and is just built well (stick drift aside, but it's not the only one with that issue, and I've yet to experience it myself so lucky me).

Recency bias is a thing, but on the other hand so is nostalgia; it tends to even out in the end.