As far as HAL goes, Wikipedia says they are owned by Nintendo. Everyone else says they are second party.
Wiki does have more to add. "Second party" as we use it really means "subsidiarity." Usually, most second party developers are owned by the parent company. Insomniac games and Game Freak are exceptions.
Still, most of the series with characters in Smash are wholly owned by Nitnendo. Also according to Wiki, the companies Nintendo owns are: Intelligent Systems, Hal, Retro Studios, Brownie Brown, Monolith, Nd Cube, and Project Sora.