I don't really think so, no. The only 3D Zelda game that rivals it is Majora's Mask, which is sort of the other side of the coin, having the elements that OoT was missing. That right there is basically a toss-up. Those two games are by head and shoulders the best 3D iterations, IMO. But I found Twilight Princess, while ambitious and attractive, to be too scatterbrained and too empty. In addition, it retread too much old ground and didn't focus enough on Link being Link. Meanwhile, even as they tried to innovate, Wind Waker had too much water and awkward pacing, and Skyward Sword was too restrictive and linear.
Now, is OoT overrated when compared to the entire pantheon of 2D Zelda games? A little bit, yes. But when I really think about it, it can deservedly be in the conversation of best Zelda because it successfully captured the essence of A Link to the Past, which is one of the most definitive Zelda games, in 3D.