No they aren't. You can't account for taste. More advanced technology isn't everything. That's a bit like saying retellings of Bram Stoker's Dracula are objectively better than the original film because they're not grainy or in colour. It doesn't work that way. They both have their own strengths. The N64 version has a bigger screen, a light controller made for palm holding, rumbling, muslim chants, cool glitches, OP deku sticks, cosmetic stuff like visible blood in the bottom of the well and Ganon's blood being red etc. etc.This list is so bad, they can't even follow their own rules.
(And yes, I know, while MM is technically a gaiden game, it's plainly set very soon after the events of OoT, and the only reason its events happen in the first place is because of a single event in Ocarina's ending. It's the textbook definition of a sequel.)
Oh, and......while I highly admire this line of thinking, why aren't the 3DS versions of both those games listed? Both of them give the games a huge visual makeover, and rework some needlessly frustrating elements (e.g., making the Iron Boots button items so you don't have to go all the way to the Equipment screen to put them on or take them off). They objectively hold up better than their original versions.
You want to make a Top ___ list, fine. Opinions are opinions and all that. But at least adhere to your own guidelines.
One does not invalidate the other. Same with Majora's Mask. The N64 version is decisively more creepy than the 3DS version.