New York City Mayor Bill de Blasio and the Rev. Al Sharpton, the civil rights leader, were among the hundreds of people mourning the 6-year-old at St. Paul's Baptist Church in East New York.
Nicholas Avitto carried a card from one of his son's friends, NY1 reported.
"I wish you would not have to die. I feel so sad that you had to die this way. I know you, Prince, are looking at me. I love you so much," the card said.
St. Hubert was arrested Wednesday near his mother's house in Queens. A crowd outside the 90th Police Precinct in Brooklyn jeered as he was led away in handcuffs Thursday night.
He was silent Friday as a judge ordered him held without bail.
St. Hubert was released from prison in late May.
Investigators have been trying to determine if he was involved in other stabbings since his release, including the killing of a homeless man on a subway platform in Chelsea last week and of an 18-year-old college student who was knifed near the Boulevard Houses last Friday night as she walked to a friend's house.