I like them both, but Skyward Sword is my favorite.
Twilight Princess is a GameCube game, by the way. It felt like an Ocarina of Time remake to me, and that's a good thing, even though it's less original than Wind Waker. Wind Waker is a better game in my opinion, by the way.
Skyward Sword is a breath of fresh air in the series, one that I loved to complete. The beginning is daunting, too long. I remember thinking that speedruns and replays would be annoying with the slow start.
Growing up my favorite Zeldas were OoT, then WW, then SS and now BotW. BotW was an unique experience, I can't imagine anything topping it off.