There's lots of casual anti-Indian sentiment, just in the othering language that's used, but there is much worse, from stories of Indians wearing the skins of freshly killed skunks, somehow allegedly impervious to the scent that makes white people gag, to four different repetitions, usually by the saintly Ma, of the horrid phrase "the only good Indian is a dead Indian."
Debbie Reese, an Indian author and educator has a series of posts on the topic of the Little House series on her great blog
American Indians in Children's Literature. You can scroll down for the list of links on the far right sidebar.