You've got it a little backwards.  Eagle Arms own Armalite, in the sense that the Eagle Arms company bought the rights to the Armalite name - and so some of the rifles manufactured by Eagle Arms are sold under the brand Armalite.  The original company called Armalite was a division of Fairchild Corporation, and has not existed for many years.

I don't know if there are quality differences between Armalite and Eagle Arms - I would imagine it's all the same parts and equipment used to manufacture them - but I do belive there are some features that only the Armalite versions may have (like chromed barrels maybe?).  I'm not sure though, so you would have to check that.

I actually got a Bushmaster (because I wanted the good customer service, in case I ever needed it) and then just ordered the green furniture as parts from Armalite/Eagle Arms.  It was pretty cheap (and I know there are other places that sell the green furniture as well).  Took about 10 minutes to change.

Eagle Arms purchased the "Armalite" name in 1995 or so, and changed the name of the company from Eagle Arms to Armalite.  There is no longer a company called Eagle Arms, but Armalite uses the Eagle Arms brand name for their "entry level" or "parts" rifles.  Component lowers are stamed "Eagle Arms, by Armalite."  You can tell if an Eagle Arms lower left as a factory rifle if there's a while eagle stamp on the front of the mag well.

Armalite-marked rifles all leave the factory as complete rifles (and are therefore all stamped with the while eagle).  You can buy a complete Armalite upper, but Armalite-marked lowers are not available seperately.  The company chooses the best forgings for their Armalite-marked rifles, and builds Eagle Arms rifles from the rest (though even these are typically excellent).

As stated, non-stainless Armalite barrels are chrome-lined, and most models include a muzzle brake.  Eagle Arms rifles are not chrome-lined, stainless barrels are not available, they come with plain muzzles, and fewer configurations exist.

Finally, Armalite rifles have a lifetime warranty, while Eagle Arms rifles and parts have a 1-year warranty.

-Troy