Police said the shooting at about 8:30 p.m. Monday was part of a gang dispute. They're searching for the alleged gunman.
The victims were identified in media reports as 48-year-old Alinson Peguero and his daughter, Alianna, of the Mattapan neighborhood.
Police say the suspect fired several times through a glass window at Peguero as he was holding his baby. They say the bullet passed through his hand and hit his daughter.
Boston police rushed the baby to the hospital in a cruiser.
They say she has extensive internal injuries and is in critical but stable condition Tuesday.
"The police commissioner is very troubled by this incident, given the young age of the victim," Boston Police spokeswoman Elaine Driscoll told the Boston Herald. "He has our detectives doing everything in their power to get to the bottom of the situation."