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.