After four years of committed bike commuting, in an effort to reduce the amount of stress in my life, I've pretty much stopped riding into Manhattan on my bike. The Brooklyn Bridge tourist congestion has gotten so out of hand, and to cut over to the West Side bike path from the Manhattan Bridge is such a congested, threatening mess, that I've reached the point where I mostly just use my bike around Brooklyn. (I've also had a series of really nasty run-ins with not only motorists, but also pedestrian tourists and cyclists doing stupid illegal things like riding the wrong way in bike lanes).
I honestly think if the City hopes to increase the number of commuter cyclists, there needs to be a re-configuration of the Brooklyn Bridge pedestrian/cyclist path (maybe give cyclists a protected lane on the car deck level). Or if that isn't feasible, we need a safer, more direct way for cyclists using the Manhattan Bridge to get over to all the protected and separated bike lanes on Manhattan's west side.
As an illustration of the commuter's nightmare that is the Brooklyn Bridge cyclists/pedestrian path, here's a video I took yesterday.