I came up with a WAG of $15MM/yr to run Citibike, based on 200 lower-paid employees and 30 higher-paid employees plus rebalancing vehicles and renting a central facility.
I then found this -
http://www.un.org/esa/dsd/resources/res_pdfs/csd-19/Background-Paper8-P.Midgley-Bicycle.pdf
Which says $1,700-2,000/operating cost per bike per year as a rule of thumb. About 6,000 bikes in Citibike, I think, so call it $12MM/yr. Ehh, it's New York, so figure higher.
I believe a major factor is how much rebalancing you have to do. If the city is hilly, people will use the bikes to go downhill but not uphill, so more employees will have to load bikes in vans and drive them to the uphill stations. Capitol Bikeshare says the majority of its operating costs is rebalancing. Manhattan is flat, so maybe that helps a bit.