You can go upstream on the Alleghany and portage to the Susquehanna River basin via a historic portage route near Emporium PA. Then its down the Susquehanna to the Chesapeake Bay; no need to go upstream. The Susquehanna as you get further downstream becomes almost a mile wide, and almost a foot deep. No commercial boat traffic to worry about and easier to find a place to overnight.
To use your earlier mentioned route of Alleghany to Erie Canal to Mohawk River would require going from the headwaters of the Alleghany to the Genesee River basin, then downstream to the Erie Canal. East on the canal to Albany NY, the Mohawk is part of the Erie Canal route. Then down the Hudson to NYC. The Susquehanna route is much shorter and would have less portages than the Genesee River from its nearest proximity to the Alleghany River basin.
The Alleghany to Susquehanna basin portage is over 10 miles, but it is done on roads and not through the bush.
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