I've got to write my own cruising guide one day but by the time I get to all of the 'spots' it will be outdated.
Your trip sounds entirely feasible and like a bunch of fun and some work.
There is a bunch of info on getting down the LI Sound available so I will only mention the Mattituck Inlet which has a free town dock at the head of the harbor (used to be free anyway). Another tip might be that if you arrive at a marina or mooring area and find a slip or mooring at or after sundown you just tie up for the night and leave EARLY the next morning and it will likely end up being for free. If weather holds you in then all bets are off.
Getting up the Hudson is pretty easy but you will want to travel mostly when the tide is with you and it is a tidal estuary all the way to Albany. The Hudson has some parts where the currents can be a bit strong but the average is about 2 knots either way (N/S) at peak flow.
Make sure your engine is up for the trip before you go. There will be considerable amounts of time in the canals you will not have your mast up.
Cheaper guest or 'transient' moorings are available in NYC from the Parks Dept. at Pier 40 and at 79th St Boat Basin for about $35/night. Try Nyack Boat Club for their guest moorings at about $25/night only 25 miles above NYC.
You will be able to write your own cruising guide when you have completed your proposed trip.
"The cure for anything is salt water~ sweat, tears, or the sea." ~Isak Denesen
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