SD - from all my reading, one of the main reasons for the Tenn-Tom Waterway was to make it possible to avoid the Mississippi. I don't recall the specific issues that were raised, but the end result was the Tenn/Tenn-Tom/Tombigbee route was better. I had researched this fairly thoroughly, as my original plan was to leave from Chicago.
Mark - sorry, no info on that. I do know you would be motoring across New York, and with locks to transit and other things along the way, I wouldn't plan on more than 40 miles a day. Been a very long time since I was up near Albany, so I couldn't really say how much sailing you'd do between there and NYC. There should be a few on here who have made the trip from NYC/New England down, so I'll let them fill in that part, as I haven't done it.