First of all, SF is surrounded by a lot of water, and Gatlon City is described to have a bay and a river/body of water (which could very well be SF and South SF. And the bay is definitely large enough for a cargo barge, like the one Hawthorn escaped on)
Cragmoor Prison, which is on an island, could be Alcatraz Island.
And SF also apparently has a subway system. Many places in Gatlon City are very... historical, and SF does have a lot of old places.
New York City also has a harbor and two large rivers and several islands (which could also be Cragmoor.) NYC has a lot history as well, and a subway system. Also apparently Marissa Meyer lives in NYC, which could make a lot of sense. Then again, Alcatraz is already a prison/tourist location. And Gatlon City is described with the term "bay" rather than "harbor," so who knows?
ALSO, I found out Galton City also has two suspension bridges, both of which seem similar to the Bay Bridge and Golden Gate Bridge, and since there are only two large bridges described, Gatlon City could very well be SF. But NYC also has a lot of bridges, and Gatlon City isn't described with a whole lot of details.
Comment what you think below.