Nine picketers were removed from protesting outside the mayor's annual "Bagel Breakfast" at the Brooklyn Public Library.
Two were arrested, and charges against them are pending. Seven others were issued summonses.
Police moved in when the protestors started to chain themselves together just after 8 a.m.
Housing Works, which organized the protest, said the "outraged bagels" were picketing what they call the mayor's lack of commitment to AIDS funding.
They believe the myor pressured Governor David Paterson to veto a bill to have low-income people living with HIV spend no more than 30 percent of their salary on rent.
Activists are participating in a 24-hour vigil in City Hall park, where the names of those who have died from AIDS are read aloud.