I think the Tonto thing is probably more controversial. For starters, given that in America we've had a history of repression against Native Americans, it instantly becomes a much touchier subject. And given that the character Tonto is basically all the stereotypes rolled in one, that makes it worse.
The Khan thing is at best just questionable, not even really that controversial. His race isn't firmly established, and he was previously played on screen by a fair skinned Mexican. It might have been nice if he wasn't a pale British guy, but I don't think it's quite in the same league as the Tonto stuff.