In my experience, when registering a boat, the physical location of the boat is irrelevant. The boat does not need to be present to sign over a title and go into the DMV for
registration. For other situations I wouldn't know, but standard titling and reg, shouldn't be an issue at all.
The sales tax issue... you'll pay tax to the state where you do the
registration. The "use" tax that most states require IF you keep your boat there too long is a different matter alltogether. If you don't move you're boat occasionally, the state it is located in will eventually want some
money. But, that has nothing to do with getting it titled and registered.