Eh, even in a city there's only so much Jack can do and Apollo is closer to Superman level than most give him credit for (and Jack doesn't have attacks for any of his weaknesses).
Apollo slowly takes the city apart...phasing Apollo into it won't do much when he's simply flying through it and destroying anything in his path. In a giant city he might be able to lay the smack down enough to kill Apollo. But my gut says Apollo 8/10 or so, especially considering his high-end showings, which are >> than even Jack's Tokyo feat.
Apollo wins, as much as I like Jack, Apollo is the best heavy hitter of Authority.
Though that's if we only count earthbound city, something like Coruscant would be entirely different story.
Well-sundipped Apollo can just destroy Mexico in minutes, I think.