Steal shamelessly from other sci-fi universes. Call them "the Rebel Alliance" or "Klingons."
Channel Tolkien (like every fantasy author since). Just throw some syllables together that sound vaguely mysterious and foreign. "Labethkor" or "Bojamdi" for example.
Go literal. Assuming a perfect translator, they would probably call themselves "humans." Revel in the confusion this causes.
Make saying the name of the race out loud an unbreakable social taboo. The player will never know!
Ridiculous, face-palm puns. "Aleens", "Shicagobers", "Danee Dovido".EDIT: Oh wait, you wanted good ideas?