By overall merit: OoT
By personal preference: MM
I agree. I definitely prefer Majora's Mask, but I can't make an argument in favor of it being the better game. If we're talking about what is the better "Zelda game" then I don't think it's close at all because Majora's Mask is such an atypical Zelda game whereas Ocarina of Time is very prototypical of the series. What I mean is how can Majora's Mask be called the best Zelda game (or at least better than OOT) if it's barely a Zelda game? As far as pure video games go, ignoring the fact that they are both Zelda games then I'd still say OOT is slightly ahead. You also have to consider the fact that MM reuses many aspects of OOT (even going as far as reusing character models) and is a direct sequel.