The Shulhan Aruch was of the view that praying Minha Gedola, meaning, reciting Minha in the early afternoon, has the status of "Be’di’abad." This means that although one who does so fulfills his obligation, it is preferable not to recite Minha at that time, and to instead pray Minha Ketana – in the late afternoon hours.
Accordingly, Hacham Ben Sion Abba Shaul (Israel, 1923-1998) maintained that if a person has the choice of praying Minha Gedola with a Minyan or praying Minha Ketana without a Minyan, he should pray Minha Ketana. Since praying Minha early has the status of "Be’di’abad," the value of praying Minha later overrides the value of praying with a Minyan.
Hacham Ovadia Yosef addresses this issue in his work Yehave Da’at, and writes that he initially concurred with this opinion. The Rosh (Rabbenu Asher Ben Yehiel, Germany-Spain, 1250-1327) wrote that he would recite the Musaf service privately if he saw that the congregation would recite it after the seventh hour of the day. Even though one who recites Musaf later than the seventh hour fulfills his position, the Rosh nevertheless felt it preferable to recite the prayer privately at its ideal time. Similarly, it would seem proper to recite Minha Ketana privately rather than recite it earlier, at the less ideal time, with a Minyan. Hacham Ovadia then dismisses this proof, noting the Gemara’s harsh condemnation of those who recite Musaf past the seventh hour. This seems to indicate that praying Musaf past that point is not only less than ideal, but sinful, and for this reason the Rosh preferred reciting Musaf privately at the proper time.
Another possible proof emerges from the ruling of the work Elya Rabba that one who needs to use the restroom at the time when the congregation prays should do so, even at the expense of praying with a Minyan. Even if a person can restrain himself for 72 minutes, in which case his prayer would be valid, it is nevertheless preferable to pray properly, after using the restroom, rather then pray with a Minyan before using the restroom. This, too, indicates that the value of praying with a Minyan gives way to conflicting concerns.
However, despite these arguments, Hacham Ovadia nevertheless concludes that praying Minha Gedola with a Minyan is preferable to praying Minha Ketana privately. Although the Shulhan Aruch indeed considers Minha Gedola a prayer "Be’di’abad," many Rishonim (Medieval scholars) felt otherwise. As Hacham Ovadia cites, the Rif, the Rosh, Rav Saadia Gaon, the Ra’aban and the Ritba all held that praying Minha Gedola is valid on the level of "Le’chatehila" – the optimum level of fulfilling the Misva. Hacham Ovadia asserts that had the Shulhan Aruch been aware of all these sources that held this position, he would have certainly ruled in accordance with their opinion. Therefore, one who has the choice between praying Minha Gedola with a Minyan and praying Minha Ketana privately should pray Minha Gedola with a Minyan.
Summary: If a person has the choice between praying Minha Gedola (Minha early in the afternoon) with a Minyan, and praying Minha Ketana (Minha late in the afternoon) privately, he should pray Minha Gedola with a Minyan.