Did Native Americans/Indians believe in God?

Hmmm.... considering that they decided to be "nice" as you said, they made that decision on their own. God has nothing to do with someone's actions - free will, remember? And as all people, not all the Natives were nice, and "compasionate" especially after they got the gist of what the Pilgrims and their descendants were trying to do. After a while, the Natives became very hostile to the Pilgrims, after all they were stealing their land.