Heather Zlotshewer, 35, was arraigned Tuesday on the misdemeanor charge of reckless endangerment and released on bail.
Zlotshewer, who lives in Philadelphia, faces up to one year in prison if convicted in the death last year of Matthew Perilli, The New York Times reported.
Just an hour before she found the infant under toys piled on top of him by two 3-year-olds, city inspectors were at the site and found it dangerously overcrowded.
Inspectors did not check the area where the infant was found Aug. 11, 2004. City Health Commissioner Thomas Frieden said he was not told of the death until a month later.
Frieden hired a new day-care bureau chief and 17 additional inspectors to eliminate an inspection backlog.