Ruono is wanted for questioning by police in connection with the killing.
He was seen leaving the girl at the bus terminal early on Monday on security footage but the 32-year-old has since disappeared.
It was only when his daughter, who is described by Port Authority Police as being in a good condition and well fed, led detectives home that they made the grisly discovery.
Stamford Police Captain Richard Conklin said that the victim, who has not been named, was a Guatemalan native in her 30s who moved with her husband and daughter to the Stamford apartment just days ago from New Jersey.
They had celebrated their move with a party for friends and family on Sunday night at the Courtland Avenue apartment.
But a domestic dispute allegedly began after the party, and the victim was killed in the early hours of Sunday morning, police say.
The family's one-bedroom home showed signs of a struggle, according to police.
The state Office of the Chief Medical Examiner investigated the scene and will determine the cause of death today.
However, police are already investigating her death as a murder.
It is not known if the child saw her mother killed.
"We know very, very little because they only moved here within the last day or two from New Jersey," Conklin said. "We are struggling to come up to speed on this very rapidly."
The girl was physically unharmed and is currently in custody of child services in New York City, the station said.
Police say Ruono had been working at the Bedford Street Diner in Stamford. Local media report that authorities have been struggling to track him down because he is undocumented.
Stamford Police will work with New York City police to investigate.
