Transport Alternatives is an advocacy group for 'bicycling, walking and public transit'. They have some great resources to reference. Crashstat 2.0 is an incredible resource that provides a GIS map with data on the number and location of pedestrian and bicycle crashes resulting in injury or death. Not only that, It also gives incredible details from pedestrian and bicycle counts mid-block and at intersections throughout Manhattan. They have a comprehensive selection of cycling resources including information, cycling tips, bicycle advocacy and legal tips.
The Bicycle Blueprint for NYC is a fantastic advocacy resource. I am especially interested in the discussion on bicycle parking at rail and subway stations. The research done by PB in NSW on bicycle parking at stations looks into this in NSW. Cycling has huge potential as a mode of access to rail stations if only there were safe routes to the stations and secure parking. The space savings that could be achieved by providing bicycle parking instead of car parking at park and ride stations could do wonders for promoting transit oriented development.