Flintlocks started replacing traditional weapons in the New World in the late 17th/early 18th centuries, and even then many native peoples stuck with the old weapons well into the 19th century. By this point, this was probably usually because they could not acquire enough firearms for everyone, but the old weapons still had their uses. The Comanche apparently briefly tried out firearms early in the 19th century and soon rejected them for their traditional bows, spears, and clubs, which were more effective from horseback than muskets.
There are apparently good reasons to assume that there were already hundreds of guns in circulation among the Indians by 1650, at least by what is presented here:
http://www.amazon.com/Most-Pernicio...WJ0_1_1?s=books&ie=UTF8&qid=1407220265&sr=1-1
And indeed pretty much the only reason bows would have been preferred over guns, of any kind, was the lack of availability. And as long as there were multiple rival european factions present and providing trade and gifts, availability of guns and ammunition wasn't much of a problem, apparently.
I'm not so sure the Comanche are making any kind of repesentative case, if that story is indeed correct. On the northern plains, guns, any guns were prized possesions, and even small numbers had a significant impact.
From what I have read on the French and Indian War, bows were pretty much obsolete by that time, and securing guns and ammo supply for the Indians, and trying to cut it off by their respective enemies were extremely important objectives.
Second, guns were never the deciding factor anyway. Bows were more effective than smoothbore muskets in both range, rate of fire and accuracy; the advantage of the musket was really that it took very little training to use, and that was never really the issue in the Americas.
I never quite got those arguments. The historical record seems to show that almost anywhere where there was a real choice between guns and bows, guns were used, even by "warrior peoples" where the time for training wasn't an issue. Certainly so by the time flintlocks came around.
How exactly are bows, of any kind, outranging guns, of any kind? Even crappy guns have a much, much higher muzzle velocity than the best bows. A lead ball is much less affected by wind and foliage than an arrow.
Even a smoothbore musket with a very large windage will put about half of the shots into a man sized target at hundred yards on the shooting stand, a distance where an Indian archer would probably not even try to hit a target.
Higher rate of fire is the only argument that makes sense to me, yet this would be more than counterbalanced by a much, much large wound effect of a musket ball compared to an arrow.
And for the skirmish and ambush type of warfare in the eastern woodlands, rate of fire is probably not much of an issue in the first place.
Arrows won't penetrate armor and shields in most cases, where only under rare circumstances armor or shields would be effective against guns.