An "outsider's" answer, first a qualification. I am not a regular commuter in NYC or any other urban area, am a regular commuter in rural fumbuck. However to keep my education current, I visit an urban area 4-6 times a year; usually for about a week- always take my bike and commute about the area. Three urban area's I try to focus my trips to are NYC, Boston and Toronto. Why those areas- because I've lived or worked in them at some time in the past & fairly comfortable getting about in them.
So why the fuss in NYC, especially manhattan ? Density. Studies have shown that too many rats packed together in a compact area - everyone gets a little edgy. Apology to NYC residents for the comparison.
During the past decade, cycle commuting in these areas [in many other urban areas also] has improved. There are more resources and facilities to support cycle commuting and the population in general has become more accustom to it. Those elements help. Some elements still hurt- cyclists are often rude to pedestrians and other commuters, plus don't obey traffic control rules and ride in erratic patterns. Motorists are the same way. Traffic controls rules, for the most part, were devised for a motor vehicle culture, not a cycle culture. Those folks with "protect & serve" written on their cars are often biased against cycle commuter - I think that is a particular rub in many areas. One would think that the protect & serve officials would be more supportive of cycle commuting; but I think it is a job security element. If there were half the cars on the street in Manhattan, fewer blue and white cars would be needed also.