Right now I've been taking 2nd ave all the way up. I start out at 135/Madison make my way to 2nd, ride it til it turns to Chrystie cut over to Bowery and one thing leads to another and I'm on the Brooklyn Bridge.
Are there safer alternatives? Second Ave is scary as hell, especially now that I am riding clipless. Is there any one else taking a similar route or heading in that direction that wants to ride together?
For a commute that long, I would go down the Hudson River bike path & cross on Chambers to the Brooklyn Bridge. MUCH safer. It's a little more distance, but the lack of stoplights along the Hudson River would probably make it about the same time.
You should also look into the East Side bike path, but it is often under construction & I rarely use it.