I feel Richard combines most of the elements which would be compelling — motive, means and opportunity. He was right there (opportunity), their death secured his own throne (motive) and means: he could kill anyone who knew (means). Henry Tudor couldn’t have done it without inside help, probably his mother, and even she would have needed assistance.  Elizabeth of York would be killing her own brothers, to ensure her ascension through marriage to Henry Tudor, a cold-blooded approach not unknown of in the English dynasty, but still. When you hear hoofbeats, don’t think zebras. Richard did it.