Stephen Glantz, 75, was charged with nine counts of cruelty to animals and nine counts of failure to provide proper food and drink to impounded animals.
In addition to the 28 dead cats found in the home, there were also 61 live adult cats and eight kittens.
All animals have been surrendered to the Islip Animal Shelter.
The house where the cats were found was deemed inhabitable.
If convicted, Glantz faces a year in jail and/or a $1,000 fine.