In the sense of most popular and longest-running, yes, but it's not the only manga with Nintendo's official seal. (Nor, if I recall correctly, is it considered to be "the" Pokémon manga by anyone other than the fans. If it is, feel free to point me to a publisher or official page that states it is.)
So, really, when you say "the manga," you could be referring to any Pokémon manga. It's just usually assumed Special because either some people think the only manga in existence is Special (see below comment on what my first post was referring to) or, which is usually the case, fans shrug off the existence of the others.
Not to mention my comment was in reference to the use of the phrase "every manga" and "all of the mangas" -- which implies every Pokémon manga out there, not just Special.