Definitely Miyamoto, it's not even close. He designed The Legend of Zelda, Zelda II, ALttP and OoT. All masterpieces.
Since then we have titles like WW, TP and SS, as well as ALBW. All of Aonuma's titles have been simply building on the OoT formula, or more recently a re-imagining of ALttP. Very little progress and I would argue regression. He introduced the divisive topic of "Artstyle" being an actual thing to discuss. His titles will seldom be heard in discussions of "greatest game of all time", unlike the Miyamoto titles which almost all heard such talk upon release.
The brightest hope for Aonuma Zelda is Zelda U, and this is again not because he is coming up with great ideas, but because he is drawing inspiration from the original incredible game Miyamoto designed so long ago.
I think Aonuma is also responsible for the stupid split timeline thing because they had to fit in the moment of insanity that was WW. Under Miyamoto I'm pretty sure it was just:
OoT->ALttP->Zelda->Zelda II
Also, for those bringing up Majora's Mask, that was the brainchild of Yoshiaki Koizumi. He was a key part of that game design (story, 3-day concept) before leaving to lead his own team.
