To this, I must sadly answer, no, Depp is most likely not the best choice to play Tonto. While do not dispute his ethnicity in any way, I must question whether he is actually a PART of these Native communities. Was he raised near one of the tribal communities he mentions above? Did he have relatives that demonstrated specific Indigenous culture to him? Has he taken part in any of the aforementioned tribal communities, either socially, culturally, or ceremonially? Perhaps he has, but I find no mention of these activities.
As many before me over the years have stated and restated ad nauseum, we must have Native American people portray Native characters. No one would suggest black-face characters any more (unless, it's making fun of that portrayal, as in the recent, Tropic Thunder), so why do we have non-Native actors working as our characters? I'm not suggesting that Tonto ONLY be played by the darkest, longest-haired, fullest-blood, "true-ist" Native person ever (I am pretty sure such a creature does not exist)...but, please, find someone that at least has both the ancestry AND the cultural ties to allow that actor the specific insight needed to accurately imbue the Tonto character as a true representative of Native American humanity.
For more on the subject, see Johnny Depp as Tonto?