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Mostly, it depends which of his appearances you're referring to. For the Series 1 episodes "the Doctor Dances" through "The Parting of the Ways" and the Series 2 episodes "Utopia" through "Last of the Time Lords", he is a companion, because he travels with the Doctor (and even has starring credits like most main companions). In his appearances in "The Stolen Earth"/"Journey's End", he would probably not be considered a companion since he doesn't actually travel with the Doctor in the TARDIS (with the exception of the scene in which all of the "Children of Time" pilot the TARDIS).

Although, what it really depends on is how you define a "companion."