It's not thst simple as it pertains to the taxes paid. You have to show what you paid in tax in the other state, prove it, then pay the difference in NY, which is always more. This law was designed primarily to prevent people from going to a state like Delaware which doesn't charge sales tax, then get a Coast Guard documentation on your new boat in your home state , say NJ.
Then if you moor there for more than 90 days you are required to pay in that state. If you get caught! Cape May is a prime example of this and enforcement officers are always walking the docks and noting out of state registration. In NY it's not such a big concern on lets say a small trailered boat because the amounts of money don't compare to tax on a 54' 2 million dollar Buddy Davis Sportfishing Yacht.
https://www.sapling.com/5994768/avoid-sales-taxes-boats