Do you have any kind of tribal ID or anything? Or at least a history of working with the community?
I understand what you're saying, and you certainly should mark the Native American or mixed-race box, but I also have heard that N.A. is one of the most-frequently BS'ed racial classifications (since lots of people have some Indian ancestry... 1/64th or whatever) so you sometimes have to be careful.
But, no, looks alone shouldn't disqualify you.