I think that has been pretty much established as a fact. Even when the Pilgrims landed in 1620, they found deserted villages where no one lived any longer.
Then, that winter they were besieged by hungry Indians so they took to the practice of burying their dead in unmarked graves so the Indians wouldn't know how many were left. That ended up being a common practice in America.
That's the winter of 1621 and might well have been a particularly bad influenza, or possibly hanta virus. However, it's the brutal winter of 1646/47, immediately following a period of drought, when the real killer disease ~ hanta virus ~ pret' near wiped out all the Indians in New England and New York (Acadia) who lived in larger villages, or even towns.
After that Indians were no longer a serious threat to Europeans on the East Coast and in fact turned to professional hunting to sell fresh meat to them.