I've done the NYC to Lake Ontario portion of that trip a couple of times, most recently a round trip from Lake Ontario down to NYC / Western Long Island Sound this past summer. I agree with Cartouche, nowhere on that route would really concern me security wise. The only times I've worried a little have been a few spots along the Erie Canal where we were the only boat docked somewhere with plenty of local foot traffic and a less than perfect vibe. But even then we've never had an issue (and the cameras have never picked up anyone nosing around the boat either).
As far as VHF licensing, you're supposed to have the FCC ship's station license and a restricted radio operator's permit to use your VHF outside of the US, although it's not necessarily enforced. It's easy enough to get the licenses though (and the RROP is good for life once you have it).
A few stops I'd recommend as cruiser friendly are Port Washington on Long Island, it's the last good stop East of NYC and very cruiser friendly (several marinas, inexpensive moorings with launch service, plenty of space to anchor, and 2 town docks to land a dinghy at). If you want to stay in / near NYC, see if you can get a slip at Hudson Point Marina. They're small, but right across from Liberty Landing in Jersey City and half the price. Docks are gated and it seemed like a good community, plus there are some good restaurants within walking distance and it's easy enough to get across to Manhattan. If you stop there, say hi to Tom on Addiction.
As you head up the Hudson, both Marlboro and Albany yacht clubs are good stops. If you have a reason to stop near Poughkeepsie, consider anchoring and dinghying ashore at the town park rather than staying at the marina there (Shadows). I was no fan of the dockmaster at that marina, plus you'll potentially be docking in as much as 2 kts of current while surrounded by people coming in just for dinner.
Once you get into the Erie Canal, walls at most of the locks are viable stopping points if that's where your timing puts you. Otherwise there are a few good options at the beginning of the canal. Waterford is always a good stop, Crescent has both the town wall and a boat club that accepts transients. Schenectady Yacht Club is very welcoming and a great stop. The town docks in Scotia are great as well. After that the next popular stop is Amsterdam although I've never stopped there personally.
Things get a little sparse after that until you cross Oneida Lake. There's not much there, but the wall at the mouth of the creek in Canajoharie is usable and Little Falls is a decent stop, although I don't understand the hype around it. I'd avoid Sylvan Beach (there were a few security issues there this past summer plus it's a party town and usually crowded) and if you need to stop before crossing Oneida Lake, go for either the east wall of Lock 21 or the west wall of Lock 22. We've stayed at both and they're quiet and isolated, but perfectly usable stops. The wall at 22 has good tie up options, 21 requires getting a bit creative.
Once you get across Oneida Lake the town docks in Brewerton are good, plus you have a few good marinas and boatyards there. Phoenix at the bottom of the Oswego Canal is always a good stop and the locals are very welcoming. There's not really anywhere else worth stopping until you get to Oswego at the top of the canal. We usually stay on the wall between locks 7 and 8 in Oswego, as it's more protected than just about anything in the lower harbor and as long as you're fine with no services, it's free.
For fuel stops, if you can get in/out of there near high tide and don't draft more than 4 feet, Coeymans Landing towards the upper part of the Hudson is usually a cheap fuel stop. Call them and ask for guidance on the channel going in, it's not necessarily obvious and the place is shallow. Next cheap fuel is in Brewerton, usually either Ess-Kay or Winter Harbor are the cheapest (and possibly the cheapest you'll see the whole trip). Oswego is usually reasonably priced as well, and I'm pretty sure there's a reasonably priced fuel supplier in Clayton (Thousand Islands). After that I'm not sure, and fuel is usually more expensive in Canada, so I'd plan to leave that area fully tanked to minimize what you have to buy before you find another cheap fuel stop.
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