So, I am somewhat aware of some syncretic movements among native americans (like at least part of the Ghost Dance movement) and obviously missionay activities and attempts to convert native americans was an ongoing effort by european imperialists, what I know a lot less about is how these efforts were recieved by native american groups. Did native american converts tend to join nearby "white", churches? It is often talked about the importance of african-led "Ethiopian" churches in the context of european colonialism in Africa, did anything similar happen among native americans?
Did there develop distinctive "native american" (or even more specifically, national/tribal variants) christian denominations?
I can answer part of this for you, with the conversion efforts of, mostly Spanish, missionaries towards the Navajo. As an non-Navajo, I have ethical issues with discussing Navajo spiritual beliefs and practices so I won't go into any details on syncreticism other than it does exist. Also, the Navajo are still not fully converted to this day, with varying belief structures in use.
The Spanish have attempted to convert the Navajo since Alonso de Banavides unsuccessful efforts in 1630. His use of the word "Navaho" is the origin of their now used name "Navajo". (The Navajo do refer to themselves as the Diné, which means "the people" but it's relationship with the Navajo title is extremely complicated and outside of the scope of this answer).
Originally, the Spanish missionaries attempted to move Navajo populations outside of their traditional borders to already established, or nearby established settlements. These efforts almost entirely failed as the Navajo returned to their own lands. However at least several missionaries attempted to set up settlements within Navajo lands and proselytize. These had marginal local successes. And this method of the missionaries going to the Navajo, instead of trying to bring the Navajo to the missionaries was something that was done widely over the Southwestern US. The spread of these settlements and their unique construction lives on today with the mission architecture style.
The first major successful effort to convert the Navajo was with the establishment of the Frisian Mission at St Michaels AZ in 1896. Interestingly, a Catholic order of Nuns, the Sisters of the Blessed Sacrament, which provided religious services to black and American-Indian populations, supported the construction of this mission.
The mission had some success, and still has services to this day. Most importantly though, was the research done on the Navajo language by missionaries. The Frisian missionaries published "An Ethnologic Dictionary of the Navaho Language" in 1910, based upon their work on the then reservation.
More controversial, many missions contained boarding schools. These are generally notoriously known among the Navajo for their use in brutal forms of cultural assimilation and annihilation. The boarding schools were much bigger implements of US imperialistic policies than the missions, but they are somewhat related.
I do not have a comprehensive list of which schools and missions outlawed the use of the Navajo language under severe punishment and which did not (And as quite a few of both are still open and litigating, I will avoid any generalizations). However the Carlise Boarding School, which was the model for all BIA boarding schools and to which many Navajo were sent, was infamous for stamping out all traces of traditional culture. Carlise used before and after photos as a way to advertise their "successes", such as this photo of a young Navajo man: http://carlisleindian.dickinson.edu/sites/all/files/styles/display_collections/public/image-teaching/scis_0006_0.jpg?itok=YPH3iBBk this was part of the Federal government's policy to "Kill the Indian, save the man."
I've spoken about it in my other posts about the Navajo, but the Navajo alphabet comes from the need of missionaries to publish bibles in the Navajo language. Eventually a standardized alphabet was used. There were other attempts by anthropologists to make an alphabet for Navajo and other Athabaskan languages, and while possibly more able to be accurately written, they were not practical for the missionaries printing bibles on standard Latin alphabet printing presses and were as a result, never really adopted or used.
I will say that the missionaries never successfully fully converted the Navajo (or the Hopi for that matter). And there are widespread efforts to this day to convert them. Over the last forty years, the Navajo Nation has seen a massive increase in LDS missionaries. The Navajo and Mormons have quite a bit of bad blood between them. Lee's Ferry, just outside of Marble Canyon AZ, was a hot spot for issues between the two. However more and more Navajo are turning to this religion today.
I'm sorry I can't answer the main question of your answer, but I hope this was of some help.
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Recommended Readings:
The Book of the Navajo by Raymond Locke
Of Saints and Lamanites: An Analysis of Navajo Mormonism by Steve Palik
An Ethnologic Dictionary of the Navajo Language by the Fransician Fathers
Dine Bizaad Binahoo'aah: Rediscovering the Navajo Language by Evangeline Parsons Yazzie
Kill the Indian, Save the Man: the Genocidal Impact of American Indian Residential Schools by Ward Churchill
I have not read this, but I have had it highly recommended to me on this topic: Navajos in the Catholic Church by David Burgge
