"We recently bought a boat in North Carolina. It is a U.S documented vessel. "
No, I don't think it *is* a documented vessel anymore. It was one, but that ended when you bought the boat. The rest is just paperwork.
Yes, you can register it with any state (as opposed to documentation) or you can do a Canadian flag option on it. If you register it in a US state, the boat can stay here without any permits, but you will probably be charged a state sales tax, use tax, or property tax, depending on the state and the address you supply for the paperwork.
You'd have to check that out with whatever states you have in mind. Usuaully, a boat has to be registered in a particular state if it remains there more than 90 days in a row, sometimes more than 183 days of the year, the terms and period for that also vary. But if you plan to keep and use the boat in one particular state--that's the one you'd register it in. If you move it from year to year...you have to look carefully at time periods and state regulations. And insurance, since insurers often want to know where a boat will be.
If you put a Canadian flag on the boat...you'd have to ask your own national and provincial tax authorities about that, but the boat will have to leave the US for 15(?) days at the end of one year. You'll need to apply for a cruising permit, good for one year, then leave, re-apply, possibly be allowed back for another year...and repeat.
Either way--you'll need the proper paperwork, signed title transfer, possibly notarized bill of sale, etc., from the PO. If you're not sure which way you will be going, pin down the PO, get all the possible options signed and if necessary notarized, to avoid "paper trail hell".