While Philippa Gregory never makes it clear just who murdered the princes in the text of The White Queen itself, she strongly suggests Richard III is not guilty of their deaths. While Richard is largely an antagonist to Elizabeth Woodville in his desire to take the throne for himself, Gregory does not present Richard as an inherently evil person as William Shakespeare or other authors in the past have done. Instead, Richard is a quiet, sensitive man, presented with some level of ambiguity. Rather than seeking the throne on his own, he is pushed to do it by his wife and others.
Richard's innocence is all but sealed for the audience when he confesses to Elizabeth that he did not commit the murder or harm the boys in any way. The television miniseries takes this a step further, with Richard openly asking Elizabeth if she used magic to spirit the boys away, making it even more unambiguous that he was not responsible since even he cannot explain what has become of them. Elizabeth reads his manner and believes he is sincere. She even allows her daughters to approach him, suggesting a level of trust.
By making it appear as though Richard is innocent, Gregory is presenting Richard as a man in over his head in his quest for power rather than a malevolent figure who's willing to cross moral lines.