The first sentence is grammatically incorrect, so is Que très mignon !

The second sentence means "How pretty you are!".

The third sentence is right assuming "cute" means sweet, lovely. Otherwise, if "cute" means "clever" see 20goto10’s answer.

Alternatively, you can also say:

Comme c’est mignon de ta part !

so "How cute!" can be translated to Comme c’est mignon ! or Comme c’est chou/adorable/charmant !.

Note that in that meaning, mignon is always masculine. What is cute is something (ce), not someone.

The first scenario with how cute of you has nothing to do with appearance but rather with appealing cleverness. The adjective malin (to mean fin, rusé, astucieux, finaud, futé) can be leveraged here :

C’est bien malin/fin/rusé/astucieux/finaud/futé (de ta part) !

I prefer relying on bien to create the degree here instead of comme (combien, à quel point).