Monster Hunter 4 sold 8.3 million on 3DS. I’d say this has a very good chance of exceeding that.
But if we’re talking 3rd party developed software, there are many games developed by third parties that have sold over 15 million on Nintendo consoles. Of course, most of these are published or co-published by Nintendo. While technically third party games, they’re colloquially called “second party” - which actually isn’t a real thing since the second party is technically the buyer in a transaction; and third parties are creators of any component outside the first party to add to the item being sold.
But even Pokémon games aren’t true “second party” games either, since they’re only co-published by Nintendo.
You're correct that 2nd party doesn't really exist in the industry, but what actually solidifies if a game is first party or not isn't publishing rights or who developed the game, it's IP control.
Nintendo confirmed this when they listed Astral Chain explicitly as a first party IP even before owning the entire IP. If you own a controlling share (which Nintendo do because they own parts of the other companies invested in Pokemon) or half or more of an IP, it's first party to Nintendo. So yes, in this scenario, Just Dance 3 is the best selling third party.