Glad to hear it is a new-ish Kubota in your boat. You will have plenty of time to get to know it well doing the canals. 6 HP does not sound like a lot of power but the original diesel installed in these boats was only a 7 HP.
CONTESSA 26 Sailboat details on sailboatdata.com
You actually can go against the current on the Hudson. The average current in most of the river is actually around 2 knots or less for most of it. Examine this link that shows the maximum expected currents for the Ebb and Flood currents all the way from NYC to Albany: Current Station Locations and Ranges
You can use this link to look up the expected current strengths for the dates of your trip (influenced by moon etc.).
I have found that sometimes when the main channel current is running up-river that along the edges it may be doing just the opposite. Even if you motor into the main current it will just result in you getting worse miles per gallon than if the current were with you.
Joethecobbler brings up a good point. You will need to re-step your mast somewhere once you hit the Hudson. One place to do it is in Catskill and there is another place further north - someone will know the name - Hop o' Nose or something like that.
If it were me I'd re-step the mast as far north as possible so if you get any N or NW winds you can use some sails to get your southing done. Having a spinnaker might just help with this also.
Good luck. Yes, I am jealous! Always have wanted to do this trip.
Thank you all for you input. it's super helpful and a great starting point as I start to plan this journey. My boat has an essentially new Kubota Diesel 6hp. Clearly it's going to take me a while and I'll have to play the tides, but luckily I'm in no rush for once.