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They were both after different objectives.
Avatar wanted to be an American anime (I will leave it up to you whether or not it succeeded) while Samurai Jack wanted to be a Samurai movie.
They are really different, so I don´t know exactly what we are to judge here. How engaging they are? How deep their stories are? Or just stating your favorite whether its objective or not?
I personally think that objectively speaking, Avatar has a rounder story, a wider and more diverse cast, amazing action and more character development.
However Jack has a beautiful artstyle, its action is pretty heavy too, and I believe this cartoons takes more risks than Avatar. Some of the imagery can be pretty violent in SJ, even if it's just robots. There is much more death and I respect how much quietness and atmosphere it has, knowing how easily bored kids can get.
Also, how such a quiet character as Jack can be so deep and adult in many situations. I believe his character more than half the cast in Avatar.
