Do you think there is more racism towards American Indians than blacks in the United States?
I wouldn't say that the preconceived notions people have toward members of society are necessarily racist. Even if they were, there's both positive and negative forms of racial prejudice. Then there's further complexity since prejudice is a localized issue. I don't think this is a productive way of questioning police bias, but to address you're question, I have been to settings where there isn't a locally cultivated black/white (or whatever) paradigm , but the reservation has more criminal activity than the surrounding area, and has been that way for multiple generations. As an example, I can recall a false rumor told from father to daughter about someone being found with arrows in their body when she was a young teenager. Another man gestures to the implicit fear of a "big old Indian" after he had finished discussing a shooting. On the other hand, there's another person in the high crime area who's well accustomed to interacting with trespassers. They take just a little because they're poor, and this goes on as long as they stay out of the house. Of course many will argue that violence has a relationship with drugs. The police may not talk about it, but they are exposed to the bias that society introduces to them.
I'm not sure racism gets to the heart of the matter for the profiling that's involved in some of the interactions in question. The way someone carries themselves, the way they talk, the clothes they wear...These things all communicate information, and it's taken into account within the context of the setting. In my experience, the sociocultural cues tend to have a profound impact in comparison with the biological ones between members of the same sex.
Hopefully by now I've also suggested that analyzing the problem of police bias by attempting to ascertain that one race is superior/inferior to another can fail to account for the geographic and socioeconomic distribution of the people within those populations, being divided arbitrarily to a racial construct.