Hospital officials refused to release the conditions of the children on Sunday night.
The children not admitted to the hospital are in foster care, police said.
Sisters Myisha Foxworth, 24, and Pamela Foxworth, 27, of Building 304, Apartment 102 at Berkeley Gardens, were each charged with one count of child neglect, said Senior Trooper Eric D. Burnett.
Myisha Foxworth is the mother of the two girls, ages 1 and 2, police said. Pamela Foxworth is the mother of the girls, ages 6 and 7, and the boys, ages 3 and 5, police said.
Police found the children after going to the apartment in search of the keys to an overdue rental car suspected of being involved in a drug bust they made that night.
Jonathan Turk, 23, of New York, and William Green, also known as Reef, 26, of Building 304, Apartment 102 at Berkeley Gardens, were each charged with possession with intent to distribute crack cocaine and obstructing an officer, police said.
Police said they arrested the men after seeing possible drug transactions occur between people in cars parked near the apartment.
Cash amounting to $280 and a small pill bottle containing six individually wrapped rocks of crack cocaine were found on Turk, who originally identified himself as "John Carter," police said.
Police said they found $510 in cash, a pocket knife and a phone on Green.
Turk and Green were being held at the Eastern Regional Jail on Sunday night, each on $25,567 bond, police said.
Pamela Foxworth was being held at the jail on Sunday night on $10,000 bond, police said. An arrest warrant had been issued for Myisha Foxworth, who was expected to be taken into custody late Sunday night, police said.
Burnett said he was "disgusted" with the condition of the apartment.
Dog feces and torn trash were found in the back bedroom of the one-floor apartment, police said.
An unloaded rifle, a bulletproof vest and ammunition were found in the master bedroom - all within reach of the children, police said.
Marijuana smoking bongs also were found in the apartment, police said.
There was little food in the refrigerator with hot dogs and other items strewn on the stove and countertops, police said. Cigarette butts were found in the kitchen cabinets.
Two dogs found inside were taken by the dog warden because they had no food or water, police said.