Majora's Mask and Wind Waker are kind of neck and neck, and I don't particularly like either OoT or BotW but I get they'd sweep the poll otherwise.
Majora's Mask was the first game I ever beat (thanks Prima guide) and it's got enough of a special place in my heart that the overhaul to the game's aesthetic and other minor changes in the 3DS version left me absolutely tilted. I can't actually just follow the critical path when I play, I have to get all the Masks and make everyone happy, because that's what Majora's Mask is about. It is a game about making peoples' lives better even beyond saving them from a falling rock.
Wind Waker is probably 'better" thanks to the WiiU version's changes. Sailing has been so improved that it's actually fun to traverse the seamless open world, Hero Mode makes the game difficult enough that coupled with a low heart run the game can be a pretty meaty challenge, and some minor changes here and there smooth things out enough. Even the aesthetic changes still feel demonstrably Wind Waker, a downgrade for sure, but the world still feels like it should unlike Majora's Mask, and while Majora's Mask is an oddball in the series, Wind Waker was a bold attempt at getting away from the shadow of Ocarina of Time with a story about toxic nostalgia that then fell flat as fanboys rejected "Celda", so the next two games we got were dyed in the wool Ocarina successors.
The actual best Zelda is probably Link to the Past but I don't have much of an emotional connection to it.