(I was wondering this, and in the process of working it out, thought others might be interested as well.)
A faction other than your own imposes a -20% penalty to all resources generated. Gold, Food, Mana, and Research. Population grows slower, with a permanent -50/turn penalty.
Humans are easily the best at maximizing gold production, because they have access to the Treasure House, a building available after the Mint. It adds +100% to gold production in addition to the Mint's 100%, giving a total bonus of +325%. The racial penalty is applied after the bonus multiplication, so a non-native Human city with a base gold production of 10 and a multiplier of 325% would yield 34 gold after the racial penalty. A Monster city with a base production of 10 and all of its multiplier buildings would generate 32.5 gold. HOWEVER, a Monster or Undead City will have access to another Craft District they can build while the Human City is building the Treasure House. All else being equal, the Monster/Undead City should always have a higher Base Production.
(Without any +population spells, keep in mind it will take 66 turns to complete a Treasure House if starting from scratch. With Agrela's +pop spell you significantly reduce the time required, to 41 turns. Given that most of my games are "over" by at least turn 100, its doubtful that building a human city from scratch as Undead or Monster would give you that much of a boost. A native race city would generate more gold for those 66 or 41 turns, after all.)
tl;dr summary: Unless you are going to use Red Dragon Eggs (Red Dragon Eggs can yield +40g/turn for Humans), there is no reason to build a human city from scratch for gold production.
Monsters are best at food production, as they are able to uniquely build the Pub (+5F, -1G) at any of their cities, and a Fishing Village adjacent to a water tile. Additionally, their food multiplier buildings cost less gold upkeep than the Human equivalents. That said, Humans would never build a monster food city from scratch because the -20% "other race" penalty and the slower pop growth wipes out any gains. They would be better than Humans if the Undead needed to make food for some reason, however.
tl;dr summary: Only undead should ever build a non-native race food producing city, and the Monster city wins easily.
The Undead have access to two unique multipliers (the Crypt adds +75%, the Mana Vault adds +50%) and the ability to create unlimited Mana Farms (+4 each). They win in any scratch built contest.
If others have worked out when an Undead City becomes better than a native Human or Monster faction city, feel free to add it. I'll update the post when I have time later. Thanks LTK and others for pointing out corrections.