Adding to what others said:
1. Song of Drums and Tomahawks series, including main book and two companion books - Pequot War and Beaver Wars have plenty of material for smaller skirmishes between Indian tribes. They are all based on Songs of Blades and Heroes, so cutting out settlers should not be an issue that makes game bland or forces too uniform. In fact, such a premise is a basis for Beaver Wars expansion, albeit based on post-contact impact of firearms trade on Native tribes.
Pequot War scenario book, if I recall correctly, gives some special rules and equipment choices to turn the dial back to early warfare, with wooden armour and such other things that were done away with in latter centuries.
Still, it's a small skirmish system and may become cumbersome with more than a dozen miniatures a side, so not really what you are looking for. The answer may be jurry-rigging one of the large battle companions to SOBAH engine, like Forged in Blood, used for company level battles of late renaissance.
2. 1676 with Mad Dogs and Englishmen expansion are a worthwhile read, and PWYW at that, so you may read them before committing a penny towards them. They allow you to field larger forces and allow for some leeway in Indian army list compositions. It's 50 - 100 miniatures a side if I recall correctly. Still, after cutting out firearms, it may be hard to make it all that interesting.