You know, New York isn't that bad compared to a lot of other east coast cities. It's flat, the intersections are mostly predictable (only a few are insane), and they're on the leading edge of creative solutions to the tougher streets. I don't have a top commuting city, but I can understand NYC being near the top of the list. I've spent most of my time there in Manhattan and Brooklyn, and ironically found that I didn't need to go outside with the bike- the subway system there is probably the best in the country. Most of the rest of the big cities on the east coast are snarls with no better solutions than sharrows for their streets.

I've biked extensively in Portland (ME; a very pleasant but small town, just mind the cobblestones), the greater Boston area (snarly roads, not a square intersection in sight), NYC (as above), Philly (unmemorable); SF (only rideable because of the tight roads- drivers fear bikes and peds; bikes should fear peds), Oakland/Berkeley (a deathtrap), LA (Downtown/Echo park/Silverlake; pleasant when not packed with cars) and Sacramento (I don't have a personal favorite commute town, but this is near to it- it's flat, square, just the right size, and has a 35 mile multi use path completely separated from car-occupied roads, running through the middle of it like a giant artery).