The bakery was shuttered due to a "severe mouse infestation" last week, health officials said.
Public Advocate Bill de Blasio accused the city of "boroughism" for differences in inspection rates.
The diner is popular in Chelsea as a post-bar grub spot.
Inspectors found evidence of mice and insufficient protection of food from contamination.
Health inspectors shut down Open House on East Houston Street after finding live cockroaches.
Health inspectors found "filth flies," evidence of mice and practices that exposed food to contamination.
Sherman Avenue Chinese restaurant One Family was shuttered by the city last week after failing a Health Department inspection.
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