Among the best flints in N America are those from the Onondaga outcrop, a ridge of hard limestone that runs from about Detroit along the northern shore of Lake Erie, through Buffalo and as far east as Albany. Parts of it are densely embedded with black flint, which you can see where the limestone was used for building (as in southern England, where some old walls, churches etc look as if they're built entirely of flint).
Onondaga flint was highly sought after and traded long distances by Indians, from early Palaeo-Indian times. I've got quite a collection I've found in ploughsoil at several sites about a hundred miles north of the ridge, including waste chippings and finished tools. I can only assume that Onondaga flint was also used for gunflints, but I don't know - were the best gunflints mainly imported from England in the colonial period, as they are for us today? What about during the Rev War and afterwards?
I believe the best outcrops were in the Buffalo-western NY state part of the Onondaga ridge, and I know that quite a bit of research has been done on this by archaeologists - there's probably lots on the web (for a start, Wikipedia has a good article on Onondaga, with a map of the ridge).