I can only tell you the criteria I used when I picked a city for my urban fantasy work:
1 - Name recognition. This can set the tone of the story from word 1. Chicago has a gritty, windy, cold, sort of tough air to it. I've never been, but knowing the books are set in Chicago means I have a certain mindset when I start to read the DF novels. Set a novel in Santa Barbara, people are going to think warm, beachy things. Set one in New York, it's all about fast-pace and expensive living next to ghetto living. D.C. means politics and powersuits (I lived near there so I'd also think traffic jams and crime). LA is about fake people and shallowness. See what I mean? The city itself should spark some instant vibe. It may not always be the one you intend, mind you, but you can direct it some through your story, by what you choose to mention and emphasize.
2 - Places in the city appropriate to some of the scenes you want to write. If you want to write about a major incident at an airport, you'll want to pick a city with a large airport in it or very close to it. If you want a sea monster, you'll need a coastal city. If you want a hurricane, it should probably be southeast. That kinda thing.
3 - To tie into both 1 and 2, a variety of settings. Most major cities will, but some of the smaller ones aren't as diverse. New York has distinct neighborhoods, all with their own feel. Chinatown vs. midtown. Central Park. Times Square. There's a place for virtually anything you come up with while you write. Want a conflict at a major sporting event? Madison Square Garden. Someone needs to get out of town quick? Grand Central Station. High class event? Opening of a show at the Guggenheim. It's all there, and the internet means these days you can get street-level pictures of anything via Google Maps, and that's assuming the places themselves don't have their own web page.
4 - Distinct culture/flavor. Sort of like #1, this will help you write the "feel" of the city, to help it be more real to your readers. You can slip little tidbits in here and there without lecturing, and really enhance the overall impact of your scenes. "The cabbie spoke about as much English as I did Pakistani, but he knew enough to get me to Lo Ping's place in record time, even through midtown traffic. He used his horn more than his turn signal, but since that's about par for most cabbies, I didn't hold it against him. We skidded to a stop in front of a row of four-story brick buildings, all plastered with signs in at least three languages. I couldn't even see an address in the middle of the kaleidescopic Chinese characters, but I did recognize the five-foot spike of naked, crispy brown ducks next to the basket of live crabs, and knew I was in the right place." That kinda thing. Throw in some scents and sounds in an off-hand way, and you're golden. You can do the same thing with a pier district, a ballpark, a ritzy subdivision, or a ghetto slum. Distinct areas make for more evocative writing and thus more interesting reading.
