Well, I agree that Skyward Sword is a funny game, even though it has serious moments. I guess the best way to describe is that I see the humor in SS as more understated, more subtle and ironic, requiring a little more thought to see. In fact, it's more my kind of humor.
I guess Link's Awakening seems funnier, because that's the way I would characterize it in general. As a funny, silly game. But it's not like SS isn't funny, either. To be honest, it's really hard to choose between the two styles of humor, because they're so different. I do feel like LA and SS could at least be considered to be in close running for funniest, although which is funnier is probably subjective to a certain degree.