Game Freak developed Pokémon Red and Green, the first Pokémon role-playing games.
Game Freak began as a video-game magazine and later became a development company founded by Satoshi Tajiri and Ken Sugimori. Nintendo published the Pokémon games and supported the project, but Game Freak was the principal developer.
The original games were designed for the Game Boy and introduced the core loop that still defines the series: exploring, catching, training, battling, evolving, and trading Pokémon. The two-version structure also encouraged players to connect their systems and exchange version-exclusive creatures.
Creatures became another important company in the franchise, especially through production and ownership work involving the trading card game. That does not change the answer to the development question: Game Freak created the first main-series Pokémon games, while Nintendo published them.