At that time (1483) the Tower of London was the second-most important Royal Palace in England after Westminster, and was the working "office" of the monarchy. Council meetings were held there, the armory was there, the Treasury and Mint were there etc. and even the Royal Menagerie was there. Over 300 people lived there full-time and over 1000 worked there. Kings and Queens Consort were expected to reside there in the Royal Apartments in the days before their coronations and in fact this tradition continued through the reign of Charles II. Young Edward was placed in the Royal Apartments as a prelude to his planned coronation and his brother was brought to join him. After their parents' marriage was proven bigamous and Richard III was elected King by Parliament they were moved out of the royal apartments to another house in the Tower. What became of them after that is really not known to us, despite much later speculation. One thing is clear though - none of those 1000 or so people who were in the Tower every day saw or heard anything suspicious or Henry VII would have trumpeted it from his throne to prove they were dead.
Before the marriage between Henry Tudor and Elizabeth of York was arranged (and the final terms were agreed upon almost right before the battle), Elizabeth Woodville had every right to fear for her life and that of her children. Her children, especially sons, had far better claims to the Throne and would have been of considerable annoyance to Henry Tudor.
I tend to agree with Iluvbertie and Marsel's points of view; Henry Tudor seems to me a much likelier culprit - and one who had most to gain. In addition, such a brutal act would have been in his character, whereas Richard never showed signs of such aggressive character (disregarding post-battle Tudor propaganda which painted him almost as an Antichrist.).
It was Richard III almost beyond a doubt.
