The death of a 2-year-old boy is being investigated as a homicide — more than nine months after a Queens babysitter was arrested in connection with his death, police sources said Friday.

Lorena Iraheta, 24, was taking care of Jason Alvarado at her Queensboro Hill home April 5 when the boy began having trouble breathing just after midnight, police said.

Jason was rushed to Cohen Children’s Medical Center, where he died six days later, police said.

Investigators believe the tot’s death was a case of shaken baby syndrome, according to a police source.

Jason underwent brain surgery but could not be saved. A surgeon told investigators that the child suffered injuries including brain swelling and retinal hemorrhages, according to a criminal complaint.

Iraheta allegedly told the boy’s mother that Jason “had fainted,” the court papers said.

The babysitter later admitted to investigators that she “got frustrated” when Jason fell asleep at her home, so she “picked him up by his underarms and shook him back and forth to keep him awake.”

Iraheta was arrested May 7 and charged with manslaughter, criminally negligent homicide, reckless assault and acting in a manner injurious to a child. She could face upgraded charges.