Here is what I would do for a computer setup for $1k:Mackie MR8 mk2
x 2: $500E-MU 0204 Audio Interface
: $115Hsu STF2 subwoofer
: $392 shipped.
Altogether that is a pinch over $1k. I would go with the mackie because they have terrific sound quality, and the 8" woofers will give you excellent extension, certainly better than the Audioengines. It has 3x the amp power to so it can hit a lot harder for when you want to crank it. I recommend the E-MU sound interface because they will have reliable drivers for newer operating systems, and also the breakout box layout is nice and simple for two channel listening, as opposed to the cluttered interfaces of some other sound cards. I would go with a ported sub like the Hsu, because the Mackies would have such good extension that a sealed sub isn't going to go so much deeper in bass that it would be worth getting, but that Hsu will dig all the way down below 30 hz. The Hsu VTF subs are on sale right now, any of those would take you over your budget but the Q control might give you an appreciable increase in sound quality.