The CitiBike website publishes JSON data containing information about each station. I downloaded the JSON file every minute from 7:30 am EST to 9:00 PM EST today, Saturday June 1st, and then ran some analysis on it.
I define “activity” as a bike being either taken or removed from a station. The top five stations in terms of activity are (drumroll) Broadway and E 14 Street, E 17 Street and Broadway, Christopher & Greenwich St, DeKalb Av & S Portland Av, and W 14 St & the High Line. Apparently a lot of people were taking their CitiBikes to and/or from the Union Square Greenmarket on this hot Saturday in the city.
Meanwhile, the stations the most frequently empty are Centre St & Chambers St and E 2 Street & Avenue B. Perhaps they would have scored higher on “activity” if there had been bikes available to ride.
Update: The Atlantic has a nice realtime visualization of this data.