Henry VII set up an enormous campaign of state-sponsored vilification against Richard III after his death. This is because his own claim to the throne was very tenuous.
Many believe that Henry VII had the princes killed just before Titulus Regius was signed into law.
Titulus Regius gave Elizabeth of York (Henry's wife) a claim to the throne - and so gave Henry VII a claim to the throne. But at the same time it gave the Princes in the Tower a better claim to the throne than Henry VII - he had a very good reason to kill them.
Henry may have had a motive, but did he have the means? As I understand it, Richard became the princes’ guardian when Edward VI, their father, died and remained their guardian until he was crowned king. During that time when they disappeared he was, apparently, in charge of the Tower. Why didn’t Richard dispel the suspicions about him by just producing the live princes or thier remins and a legitimate explanation for their deaths? Edward VII and his younger borther were Edward VI’s sons and heirs apparent before Richard, giving Richard a motive to kill them. Thus, it appears their disappearences lead straight to Richard’s door.