The one I'm reading right now is An Indigenous Peoples History of the United States. It's U.S. history from the perspective of Native Americans. By Roxanne Dunbar-Ortiz

If you want to learn from other regions of the world, then David Bushnell's books about Colombia are pretty good. I can recommend The Santander Regime in Gran Colombia, which, despite what Bushnell himself claims, is the definitive history of the dissolution of the South American regime. But it may not be what you are looking for, since its viewpoint is pretty western - Latin America, despite claims to the contrary, is part of the western world in culture, ideals and goals and the political protagonists are white men for the most part.

On the other hand, Americanos: Latin America's Struggle for Independence by John Chasteen dedicates quite some space to indigenous and black actors, along with women, so you may get a fuller perspective of figures that are often forgotten, from a region that is often forgotten.

Outside of history, perhaps you would like to check Jorge Icaza's novel Huasipungo, translated as The Villagers. Though its author was not indigenous, he was part of an Ecuadorian literature movement that sought to focus on the indigenous and black people of Ecuador, instead of erasing them in favor of the white and mestizo mainstream. In this, Icaza is the closest to relating the history of abuse the Natives of Ecuador suffered from a non-western perspective.

There's a great book by Miguel Leon Portilla called the Vision of the Vanquished (I think sometimes it's translated as the Broken Spears) you can easily find it online and is about the conquest of the Aztecs from their point of view. Leon Portilla was one of the most important historians in Mexico, was fluent in náhuatl and he was passionate about the pre-hispanic history of Latin America (he died just last year).