You don't want anything so nasty that a group of players with whatever sidearms they would carry can't confront a group of them successfully. Which generally leads you to "man sized monsters" of some sort, unless you're willing to outfit your players with some pretty serious hardware. (Exosuits? Space Cruisers?)
Obviously something like the OTU's Aslan or Vargr make good antagonists. They're clearly intelligent, but can be ruthlessly "inhuman", destroying whole colonies with their battle fleets. Players would probably interact with them peripherally - bumping into scout ships and whatever passes for "privateers".
If you don't like the OTU's "Furries", then you can turn to other classics:
Robots/AIs (like "Mass Effect"'s 'Geth' or "Battlestar Galactica"'s Cylons) - hive mind AIs with a religion hostile to your players.
Bug/Lizard-Men (like "Space: Above and Beyond"'s 'Chigs' or Spriggan Miniature's 'SPUGS') - non-mammalian critters that want our resources but are different enough psychologically that there can be no meaningful commerce.
Xeno/Bugs (Alien(s), Warhammer 40k's 'Tyrannids' and 'Gene Stealers', HP Lovecraft's 'Mi-Go' and 'Old Ones') - Insect or Fungoid monstrosities that may not even be alive in a way we understand, but which have roughly man-sized "drones" and enough technical capability that they might be intelligent (or maybe just parasites on a living starship?)
It might be fun to do a disgusting race of slimy and unsettling *things* that are alien and horrible in every way possible, but turn out to be quite intelligent and unwilling to deal with horrors like Humans, who are clearly abominations that Must Not Be. Maybe we remind them of some pest on their homeworld, or maybe "dry" creatures remind them of their own excrement on a visceral level, and they really can't help but be repulsed by us, even after they learn that we're not just some parasite that hijacked a more civilized species' equipment after destroying them. (After all, life forms with a fixed volume skull can't possibly be very intelligent - there's no room for their vacuoles to expand!)