It's now been more than 5 years since I was last in that part of the country. Too long in my opinion - I'll have to get back soon! Anyway, to answer some of your questions:

To get to NY-3 from Cornwall, you'd cross into New York and head west on NY-37 to Messena and then south on NY-56 to Sevey where you'd pick up NY-3 east to Plattsburgh. You'll be driving through the Adirondacks, one of the last relatively untouched natural areas in the northeast, so there will be plenty of great little hikes. I'm not sure of what's within child-leg hiking distance of the main road, most of my trekking in that area has been by canoe, but poke around the web and I'm sure you'll come up with some nice opportunities easily reachable from NY-3.

Sorry, I don't know much about Plattsburgh, per se.

Waterbury and Stowe are easily doable as a day trip from Burlington. In fact, Waterbury is less than half an hour from Burlington by Interstate. If you or your wife are fans of the Sound of Music, the Trapp Family Lodge is just outside of Stowe, and has some lovely hikes. There are also wagon/hay rides that the kids might enjoy, and the Baron and Maria are buried in a small private cemetery on site.

As for which ferry to use, I'd opt for the longest boat ride which would be the Port Kent - Burlington run which departs from about 10 km south of Plattsburgh. You might as well enjoy as much time 'cruising' the lake as you can. This also has the advantage that it will be less utilized than the shorter Plattsburgh - Grand Isle run and so will be less likely to be full. In either case, I wouldn't think that reservations would be necessary.

Just one other suggestion. Look at returning to Burlington from Stowe by way of Smuggler's Notch (VT-108). It's a great little scenic road with some nice kid-friendly hikes. VT-15 would then complete the loop back to Burlington.

AZBuck