According to Josephus, Onias was descended from Juddea listed as a Levite in Nehemiah 12:11.
Yes but the thread starters quesion was to do with the legitimacy of the Maccabees to become high priests and not Onias, who it seems was a Levite. As Edward pointed out though it also seems so too where the Maccabees.
My problem with the question was why wasn't one of Onias's brothers or close heirs chosen instead;
This link seems to answer that question;
Source: http://www.chabad.org/library/article_c ... lected.htm
Ofcourse Onias's brother Jason did usurp the high priesthood from his brother, but it seems that he was unworthy(2Maccabees4:7-17). Jason was subsequently replaced by Men-e-la'us, there is some dispute about him. Josephus claims he was also a brother of Onias lll and Jason, while 2Maccabees states that was the brother of Simon from the tribe of Benjamin(2Maccabees3:4, 4:3). As we Catholics regard Maccabees as inspired we would have to go with the account from Maccabees. The Jews also accept that Josephus was more than likley confusing Simon(or Simeon) the brother of Men-e-la'us with Simeon the father of Onias and Jason.
Source: http://www.jewishencyclopedia.com/artic ... 9-menelaus
The other question that I had in mind was, who exactly chose the high priest if a heir or brother of an existing high priest was considered unfit, the previous link that I posted seems to be correct in stating that the king could do it(1Kings2:26-27, 1Kings2:35). Where it is possible that the king could not do it, it seems that the Sanhedrin would have a say in who was appointed high priest.
I still don't understand how a non Levite such as Men-e-la'us could be considered a legitimate high priest though, but then I'm not sure about Caiaphas either. I'm pretty sure his father in law Annas was a Levite, but would that have made Caiaphas a legitimate heir, it seems that God still used Caiaphas to prophecy for example(John11-49-53).
It is also interesting that some Jewish traditions claim that Solomon replaced Abiathar with Zadok, because the Holy Spirit had left Abiathar and he could not longer consult of the Urim and Thummim, which gave the Jewish high priests a kind of pseudo infallibility.