I found Twilight Princess to be the easiest by far, and by far the easiest 3D Zelda, period. It was blatantly obvious from the get-go how to beat the TP bosses, and I beat the game at 100% completion with very few issues. The puzzles seemed extremely simplistic, but what annoyed me the most is that a lot of the time, rather than opting to create more difficult or ornate puzzles, Twilight Princess seemed to just give the illusion of difficulty by bloating the dungeon size and turning it into some sort of repetitive labyrinth-like structure (*points to City in the Sky*). I found the side quests, too, to be incredibly simplistic and easy. The combat was also a breeze, both in boss fights and out; the only boss that gave me serious trouble was the mini-boss guarding the Ball and Chain in the Snowpeak Ruins.
That's not to say that I thought the game wasn't all overly simplistic; it certainly had its shining moments of ingenuity, notably Arbiter's Grounds and Snowpeak Ruins.
Wind Waker, by contrast, brought a lot of new things to the table with sailing and a great expansion on the exploration component of the Zelda franchise, adding a nice aspect of non-linearity. This gave the player the sense of true adventure, never being certain where they would wind up next. The dungeons were certainly more difficult, with some interesting puzzles in the Tower of the Gods and the Wind Temple, who both had multiple layers to their puzzles; the real stand out of the game was the Earth Temple, which was reminiscent of both the Shadow Temple and the Spirit Temple from Ocarina of Time. The light-based puzzles are almost always my favourites, because it involves the manipulation of many different factors to get the proper end result. I also found the bosses to be generally harder, particularly the final battle in WW compared to the final battle in Twilight Princess. The final battle of Wind Waker was truly engaging and exciting for me, but the Ganondorf battle at the end of Twilight Princess felt drawn out and forced by the time I'd finished.
To reiterate, I think Wind Waker was most certainly the harder of the two in nearly every regard.