I'm not too sure about this. The stock subwoofer may be a different spec than most other automotive subs. For instance, if it has a different Ohm rating it could draw more or less current from the amplifier resulting in damage to the amp (V=IR so V/R = I).
Also, it is likely to not have as beefy specifications as most of the production speakers and replacing it with something off-the-shelf could sound horrible.
I recommend going with a bose replacement speaker as opposed to just slapping something random into the factory system.
http://www.courtesyparts.com carries them last I checked, you can also likely find a bose factory sub on ebay.