I was just wondering what is the best controller to use with Metal Gear?

I guess it's a sony controller ??

personally, I can't support the "shape" of Sony's controller : it gives me cramps !!
So I play with an good old Xbox one controller !!
It's up to you....

So far I've used my two dInput controllers successfully without any problem. Didn't try my Xbox controllers, but I guess they should work fine as well. I'd say use whatever works for you and configure button layout yourself for best experience.