From the BNY website section on "Rules and Security"

"Carry only what is necessary in panniers (saddle bags), handlebar bags, and/or bags that attach to the back of the seat. Backpacks are not recommended; if used, they must be very small. Bags are subject to search. Please cooperate if federal, state, or city officials ask to see the contents of your bags."

I've seen people with backpacks. Never seen anyone stopped for a search