Option 1:
Steal shamelessly from other sci-fi universes. Call them "the Rebel Alliance" or "Klingons."
Option 2:
Channel Tolkien (like every fantasy author since). Just throw some syllables together that sound vaguely mysterious and foreign. "Labethkor" or "Bojamdi" for example.
Option 3:
Go literal. Assuming a perfect translator, they would probably call themselves "humans." Revel in the confusion this causes.
Option 4:
Make saying the name of the race out loud an unbreakable social taboo. The player will never know!
Option 5:
Ridiculous, face-palm puns. "Aleens", "Shicagobers", "Danee Dovido".
EDIT: Oh wait, you wanted good ideas?