MyAnimeList claims that Ray is a side-story of Black Jack, while Wikipedia takes the more conservative approach of just saying that they're related. However, it's not clear whether Ray is canon material in the Black Jack universe (and if so, in what sense). In any case, Ray mangaka Yoshitomi Akihito is on good terms with the current license-holders of Black Jack, and has produced his own version based on the original but with his own artwork.
Because of copyright reasons, Black Jack was only alluded to as BJ and never seen fully in the original manga, but because the anime was produced by Osamu Tezuka's own studio he is able to appear fully in the anime (though still somewhat obscured) and be referred to by his original name. Interestingly, in Black Jack 21, the sequel to the Black Jack anime, Black Jack was referred to as "BJ" by the assassins hell bent on killing him.
As far as I can tell, there's no official word on what the relation between the two are, so it's sort of a matter of opinion whether it's a sidestory or just a homage. My opinion is that, by animating Ray, it was more-or-less retconned into the Black Jack universe, or at least some alternate universe, so I think it can be elevated to the level of a sidestory. However, that was a decision made by whoever the current rights-holders are for Black Jack, and while it's valid in a legal sense some might argue that it shouldn't be considered a side-story but a homage. Tezuka manga purists could very-well object and describe it differently, as everything related to Ray (manga beginning in 2004) happened well after Tezuka's death in 1989.