Officers discovered 50-year-old Ikechukwu Augustine Okeke and 54-year-old George Orji inside the Dish Network offices on Yonkers Road.
The offices were damaged in the April 16 tornado and are unsafe for entry, according to city code inspectors.
The men are charged with felony looting in addition to second-degree trespassing. Okeke also faces a breaking and entering charge and is being held in lieu of bail. Orji's bail is set at $9, 000.