Oh man, this is so cruel!
It's a very difficult comparison because despite singing in the same band, they are two very different types of singers. I think back in the day, Jon had more range and versatility, being able to shift between sounding like John Lennon and Ronnie James Dio at an instant, but Zak's technique was (and still is) better and more professional, and he's no slouch when it comes to variety either. His smokey, Southern-style vocals are just as strong as his Geoff Tate-esque wails, and he was certainly better suited to singing the mainstream ballad songs (which came to dominate the Savatage discography after Gutter Ballet) while still being able to handle the more metal materiel.
Overall, looking at the entirety of their careers, I think Zak has held up better as a vocalist. While they are very different, and this comparison is to a certain degree more of a matter of taste then anything else, I think it can safely be said that while Jon Oliva was a better frontman, artist and songwriter, Zak was (and still is) the better singer. To Jon's credit, I do enjoy listening to his post-Savatage records more then Zak's, mostly because I do think he is the better songwriter, but based purely on vocal performances, I have to give this to Zak.