I've been working on the same genre and also have struggled with rules. So far I own:
The Sword & the Flame variant – First rules I tried and although I love these rules I didn't like how they played for the Old West.
Warpaint – Haven't tried these yet although they'll be next up when I go back to the Apaches (I'm obsessed over WW3 atm). These rules use "quality dice", like Force on Force and I kind of like that mechanism.
Space 1889 – I really like this set of rules. I ignore all the Martian sci-fi aspects and just use them as a set of colonial rules. I think with some "chrome' added for a more Apache feel these might work.
Too few to fight too many to die – Haven't played and as it's targeted for multi-figure bases, although there are some things you can do to fake it with single based figures, I've decided to skip these.
Yellow ribbon – A very well regarded set of rules. They are a bit hard to find and are definitely old school in presentation. They also require order chits which I'm not a huge fan of but they have rules that force the Native American side to fight more historically.
Legends of the Old West & supplements – Fun and fast, not terribly historical. Smallish sized forces, i.e. it will probably bog down if you get past 20 or so figures per side.
;tldr version, I'd look at Yellow Ribbon or Warpaint. Here's a website that lists a lot of possible rules.
link
