From http://iroquoisindians.freeweb-hosting.com/webdoc71.htm It looks like the chief Skenandoah of the Iroquois nation lived in the late 18th century. Date mentioned was 1794. I suspect that the song would have been written either around that time or after.

So, to answer carol1211k, I don't think it likely the song would have been heard BEFORE the Lewis and Clark expedition, but more probably after it.