They sound quite evenly matched to me. My first thought was Majora, but now that I think about it, I'm actually going to go with Vaati. If I remember correctly (it's been so long since I beat MC), Vaati's pretty much invincible while his eye is closed. Majora primarily relies on physical attacks (again, if I remember right) aside from those spinning tops and his whips. I think that his main mask form might have a laser attack, which would effectively work in a similar manner to arrows, but once he's damaged enough by Vaati, that ability seems to disappear in his other forms. Plus, there are times where Vaati needs to be hit in four different places at once. I suppose the boss masks might be able to help with that, though...
...I had trouble with both bosses, to be honest, so whatever.
