There are over 500 federally recognized tribes in the United States alone, and most of them have different languages, cultures, and religious beliefs. Is there a particular tribe you're interested in learning about? It would be difficult to answer this question with generalizations without accounting, at least, for the major regional differences (plains, southwest, woodland, etc). There are some similarities amongst tribes of those regions, but many nuanced differences as well.

Source: am Oneida

As /u/yakshack said, there's an extreme amount of diversity of beliefs to deal with here. It'd be best if you narrow the focus down a bit, because otherwise it's like asking "What gods did Eurasians believe in throughout history?"

But since you brought up the word "manitou," I figure I might as well give you some context for what that is.

Manitou is a spiritual concept originating with the Anishinaabe peoples - the Ojibwe (Chippewa), Odawa, Potawatomi, etc. - north of the Great Lakes. It can mean both "gods / spirits" and "spiritual power."

The Gichi-Manidoo ("Great Spirit") is the supreme god (though its possible that previous, the gichi-manidoo was more of an abstract unifying force in pre-colonial times and only became entity due to Christian syncretization, but that's a theological debate I'm not equipped to tackle right now). In traditional Anishinaabe thought, the world is populated by a host of lesser manitou. They can inhabit sacred sites and sacred objects, and led their power to men and women when appropriately called upon.

Such holy people are also manitou, in a sense, being imbued with spiritual power. This is why in the colonial records you'll occasionally hear about Jesuit missionaries being referred to as manitou. The Anishinaabe didn't considered them to be gods, just as foreign priests carrying their own spiritual might with them.