The mom killed the kid.....
So much of the story points to that. We are led to believe it might have been the uncle, Jason the mom's brother who lived with her and Nickolas but he has been dead for 16 years so why the need to protect him?
Why would the sister especially go to such great effort to protect a drug addicted older brother who killed her younger brother? She would not. She would protect her own mother though.
The mother had a heroin problem at the time. She has said that Nickolas was very troubled and violent towards her. I doubt it would be premeditated but perhaps she struck him in a rage and he hit his head or something. The brother Jason probably helped do something with the body.
I totally agree with investigator Charlie Parker who believes that the kid was killed in that home. He's trying to find the body but the authorities don't seem to care.
FYI something that was not mentioned in the film but i have read online is that the 1998 death of the uncle Jason by a drug overdose may have been suicide. Charlie Parker believes that his investigation caused this. I wished this was mentioned because it matters.