I generally use CitiBike as the first and last mile (or two or three) of my daily commute, which starts/ends with the LIRR at Atlantic Terminal. For my daily commute to the Brooklyn Navy Yard (where we need more docks so they are not so congested and I can get some more Bike Angels points 😊) it's Vanderbuilt Avenue. It;s all downhill from Prospect Park to the East River and a fun and snappy ride.
When I head into Manhattan the Manhattan Bridge is my path of choice. I have not yet been on the new Brooklyn Bridge cylce path, and the Williamsburg Bridge is a bit too far north for my commutes, but the MB drops you right into an area with great bike lanes and infrastructure.