"Best" is a term based rooted firmly in opinion. I have four favorite Zelda games, and I love them all dearly for different reasons, but as for the best Zelda game, I think I'd go with Wind Waker.
The main reason for this is that I felt like Wind Waker, out of the games I played, was the only one that felt like a complete thought. There was nothing missing from the game (semi-open world exploration, side quests, charming, lovable characters, challenging dungeons, etc etc). But the thing I felt most impressed by was that each of the islands felt like they belonged in the same world. Everything was coherent in terms of music, characters, and dungeons. Unlike Skyward Sword, where there were three entirely different ecosystems for you to explore, Wind Waker's variations felt more subtle, eased in the transitions by multitudes of islands displaying the changes in landscape. The game was inspired by celtic folk tales, and you could obviously tell from the music and style of the entire game.
Not to diss on other Zelda games, of course. I've played many, and I've loved them all. But in terms of overall greatness, I'd argue that Wind Waker really sets the standard.