Baxbeaux has a location downtown on Mass Ave. and I’ll throw in another vote for their pizza. Iaria’s pizza isn’t bad but I really don’t like their food otherwise.
Southside has the new BJ’s Brewhouse at Greenwood Park Mall. It’s a chain restaurant (not just a pizza joint) but they have a very good deep pan pizza and they brew their own beer and root beer.
Southeast in Wanamaker is the New Bethel Ordinary. I would compare their pies to Union Jack… lots of cheese, very thick and very tasty.