S8472 is tough enough to beat the Borg.
The Vong can take on the Imperial Remnant.
Both rely on bio/organics in ships, weaponry, etc.
Which would win?
C’mon, guys! Nothing?
SPOOFE?
Vong. The Vong killed Chewbacca, whereas 8472 NEVER killed anybody of import on Voyager.
…not that there WAS anyone of import on Voyager… 
You might get a better response posting here:
http://forums.comicbookresources.com/forumdisplay.php?s=&forumid=30
Wow, tough question. Both sides come from the later works of thier respective franchises, long after both had passed into irredeemable suckitude. So the universal rule that the cooler franchise automatically wins is right out the window. Which works in Star Trek’s favor. 
Hmm. I’d have to say that the Amnion would kick both of thier asses.