I'm not sure, we're travelling into "what if" conjecture, so really who knows? The East Coast tribes were in general pretty advanced, perhaps not technologically but socially/politically they were fairly advanced (If I'm not mistaken the Constitution was heavily influenced by the Iroquois' system of government), and the Plains Indians certainly turned out to be excellent light cavalry. While it's certainly true the American Indians were clearly unprepared for European style warfare, I am a firm believer in the idea that a warrior can defeat a soldier but soldiers defeat warriors, firearms back then were crap and certainly not a be all end all weapon. Guns only took off because they were cheaper to build, maintain and train with then arrow weapons, they couldn't reload as fast as a archer and didn't have near the penetration of a crossbow. If they had pre-plague numbers they certainly could have wiped out the early colonists, Jamestown and Plymouth only survived their initial winters due to the patronage of the local tribes. Plus the way the local tribes would have handled the European incursion probably would have been different if they weren't coming off a giant cataclysm.
The problem is that their actual performance, even after a century of familiarity with firearms, does not bear out their being able to accomplish anything with the extra numbers. The engagements of the French and Indian War proved that a detachment of British regulars, or even colonial militia, could stand, fire by rank, and not a single person would ever reach them. The natives would break under a single volley of musketry. Engagements where they in theory had the numbers to push through they could never coordinate sufficiently to leverage their numbers on the field; instead they committed, and were broken, in small waves. The only successes they ever had were against units caught in marching formation, and even that didn't always go well.
While they might have successfully destroyed the early British colonies if they were in the mood to (a more difficult proposition than it sounds, really, since they're going to have great trouble with even the most primitive of European fortifications), that buys them very little as the Dutch will lodge anyways and New Amsterdam will be taken in the Anglo-Dutch Wars and become New York regardless. In the end, it earns them the enmity of the British Empire and merely ensures their complete destruction at the hands of the British Army sometime during or before the 1730s.
