I honestly believe that Zeus is the best Boss to farm, but I have never been to places such as Briskbreeze tower, Waterworks, and the other two dungeons in Aquila. In the more lower level parts of WizCity, I do prefer lord Nightshade.
In Wizard City, you can farm Lord Nightshade, Sunken City, the bosses on Cyclops Lane and Colossus Blvd, and (for not-so-great gear, but a cool housing item and a myth sprite), Prince Alicane on Firecat Alley. Depending on your level, Briskbreeze is good, but some of the gear is no-auction.
Other than the Aquila dungeons, I think Waterworks (specifically Luska Charmbeak and Sylster Glowstorm) is the best place to farm in Wizard City. They drop Waterworks gear (super useful), mastery amulets (again, super useful), legendary gear (which can sell for big bucks), plus some basic stuff like pet snacks, treasure cards, etc.