It seems rather unfair to compare the two. Not only are both excellent experiences in their own right, but each is so radically different from the other I don't think they can be categorized together for comparison.
Regardless, Ocarina of Time is, to forgive the cliche, timeless. I think it has longer lasting appeal over Majora's Mask. I think Ocarina's nostalgia factor is stronger, though simply by virtue of having come first. I think Ocarina's themes, story, characters, and events resonate with people stronger today as well as then.
Majora's Mask is a wholly unique experience and almost incomparable to anything else, really. It has its own memorables that stand out on their own merit. It functions, looks, feels and plays almost entirely differently to other Zelda games and almost any other game for that matter. Everything it does it excels at.
But Ocarina's timeless appeal and the she sheer impact it made on gaming not just at the time of its release makes it the superior product, imo. But comparing the two is like comparing apples and oranges.