Zeller is better than both.
Sounds like you haven't seen either play. Baynes is a rugged player and does a lot of things that don't show up in the stat sheet. For example, he's a very good low post defender, boxes out properly, sets massive screens, and has soft hands. He's also an agitator that gets under opponents skin.
However, let's take my opinion out of it and see what Van Gundy had to say about Baynes following the Boban signing:
“Aron is a really good player and I said this after the last game, we’re going to be in a difficult situation by the [CBA] rules of trying to re-sign him next summer,” Van Gundy said. “I’m supposed to downplay him, not play him up and tell you, ‘You know, that guy’s a pretty solid backup,’ but the bottom line is he’s a starting-caliber NBA center who we’re very lucky to have as a backup.”
“Now he’ll make about triple next summer of what we’re giving him,” Van Gundy said in November. “We won’t be able to re-sign him, but the critics, who always know, killed us for overpaying him. Right now, we could trade him to 29 teams in about five seconds right now at what he’s making. So I don’t think we made too bad a deal.”
This summer Boban was signed for 3 years at 21M. Compare that to Zeller who in the same market and playing the same position was only able to garner a 1 year 8M deal.