We'll never know. The princes are seen less and less of until finally being confined indoors and then never seen again. Richard certainly has a motive as at that point they seem like the best possible claim to counter his. Certainly any revolt or plot would likely have used them as a figurehead.

He's also lived to see Henry VI kept in the tower only to be the focus of plots and attempts to put him in the throne. His brothers leniancy towards his enemies often came back to bite him as well.

In the end it could have been him, he could have ordered it, maybe someone thought they should do it on his behalf without him knowing. To my mind the first and last are helikely and the most likely is that at some point they were killedd on his orders.