Off the bat, both HSU & SVS are well-regarded companies in the home theater subwoofer business. Their products blow away anything bought commercially.
Everyone in the home theater (HT) world seems to have their favs though. Think of the Camaro vs. Mustang arguments (both good cars, but zealous fans on each side). Let's just say that SVS has the most zealous fans of the 2 companies (for good reason, their products kick butt).
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The Stereophile award only accounts for products which pay for advertised in their mags typically (HSU is one of them), no SVS products I think were in that review.
SVS 20-39PC has been independently tested to perform better (SPL or loudness-wise) than the VTF-3. Gotta get past the cylindrical look of the subs though (I did, I got the 16-46....looooooow bass for me!). SVS does have traditional looking square/rectangular subs (like the VTF-3) if that's your fancy too.
Heck, even the cheaper SVS 25-31PC performed better marginally to the VTF-3 (although the HSU sub could go a tad lower in frequencies below 20Hz), but hundreds cheaper that the VTF-3
Read a review here comparing the VTF-3 vs. the SVS 25-31PC (& another competitor) here:
http://www.svsubwoofers.com/reviews_mitchell.htm
Here's a discussion thread on one of those HT forums that talked about both subs (HSU & SVS options).:
http://hometheaterforum.com/htforum/showthread.php?s=&threadid=151597&highlight=VTF3+and+2039
You can also have someone build you one for that cost that will tear-up any commercially purchased sub. These 2 folks are well-known builders (they both are long-term stalwarts in many of the HT forums) that have many, many satisfied customers (& back-up their work):
http://www.acoustic-visions.com/~acoustic/
http://www.rutledgeaudiodesign.com/