The volume of a subwoofer is proportional to the amount of low bass it can produce. So, if you want low bass, you'll have to have a larger subwoofer. The computer 'subwoofers' currently out there don't go very low at all (maybe 50-60 Hz), so looking for a smaller one wouldn't be too productive in terms of sound quality.
You could move your sub to the floor to free up desk space if it helps.