i think new york is decently friendly to cyclists. but is ultimately kind of like an acquaintance that invites you to a party but then basically ignores you after you show up. you might get a drink or two out of the deal but then you wondered why you bothered to show up at all.
that said, i don't think it's the fault of the planners. nyc has been making tremendous strides in planning for new bikelanes and making biking safer. i think it's more the attitude of non-bikers that double park in bike lanes, don't look before pulling out of parking spaces, and generally treat cyclists like they have no right to be on the road. which surprises me in a place like brooklyn, where you can't go five feet without falling into a bike shop.
i think more education is needed, to show people how fun and healthy cycling is, and also to let drivers know that yes, cyclists are on the road, they have a right to be there, and should be treated as such. and in turn, cyclists should also remember to obey traffic lights and not barrel into pedestrians. and stay off the sidewalk! (full disclosure: i do ride on the sidewalk sometimes, but slowly and carefully if pedestrians are around. it beats getting squashed by an SUV in sunset park, even if it is a crummy thing to do.)
and san francisco may have a lot of cyclists, but it has the most insane traffic of anywhere i've been. i don't know a single person there that hasn't been hit by a car while walking or biking- also, the streetcar tracks are a total hazard, a friend of mine faceplanted last week after getting her wheel stuck in one. so i'll take nyc any day.