Take a look at the 3 volume Colombian Consequences set, edited by Thomas
(Smithsonian Institution Press). Native Americans in the Spanish empire had
an entirely different legal position from plantation slaves. Following the
Pueblo Revolt in the Southwest and the reestablishment of government there,
the Pueblos generally became allies of the Spanish against nomadic Utes,
Apaches, Navajos, and Comanches. both found common interests in preserving a
sedentary life style.

There are several examples of revolts in missions of the northern frontier of
New Spain, usually the result of ignorantly placing traditionally hostile
groups together in the same establishment (similar to conflict between
hostile prison gangs today). These revolts were often not directed against
the Spanish so much as the "enemy," though the Spanish received some fire as
they were the authorities responsible for enforcing this cohabitation. The
Chumash Revolt of 1824 may have been inspired by an outside Russian agitator,
Prokor Egeroff.

I am constantly amazed by the many more frequent examples of cooperation as
opposed to resistance in the Spanish empire. After the Spanish reestablished
themselves in the Southwest, they were generally rejected by the Hopi, except
for those in the village of Awatowi. This resulted in the other villages
massing to burn all the adult Awatowi males in their kivas and carrying off
the women and children (presumably for "reeducation" elsewhere). Native
auxiliaries were used often by the Spanish and French, and even by the
British in warfare. The situation is so much more complex than that of
plantation slavery.  Resistance took many subtle nonviolent forms. A
fascinating topic!