NYC to Waterford, NY the beginning of the Erie Canal is 3 long days or 4 shorter days plus time to unstep the mast and secure it.
Erie Canal from Waterford to Buffalo, NY will be 7 to 10 days. It will take a few days to get the mast stepped again in Buffalo.
Can't help you for the Buffalo to Milwaukee part.
From NYC to Kingston, NY is one very long day. Stay at the Hudson River Maritime Museum it is a cool museum and a nice place to stay. I've stayed there a couple of times. A short walk away are a number of good restaurants and a great ice parlor.
Kingston the Catskill is another long day, this is where you get the mast unstepped. How long that takes is hard to tell. Depends on how prepared you are with mast cradles and how busy they are.
Catskill to Waterford is another long day. Tie up at the Waterford Visitor Center just before entering the canal. A grocery store is about a mile away and they let you take the cart back to your boat. The grocery store will come and fetch the cart.
Leaving Waterford at the first opening (around 7:00 am) will get you to Baldwinsville in about 3 ½ long days. From there it is about 4 to 5 days to Buffalo.
Do subscribe to the Canal's Notice to Mariner's and do review their site carefully lots of good information there.
Whether by water or by land, explore hundreds of miles of historic waterways and trails. Adventure awaits on your next excursion along the NYS Canal System!
www.canals.ny.gov