If all you want is more bass, I would definitely go with a decent 10" sub and a well matched amp. Make your own box from 3/4" MDF.

If you are very handy, you could fiberglass the box into the side of the cargo area, something I hope to do in the near future. Otherwise just put some quick connects at the box so you can pull it out when needed.

A decent 10" with some power put to it should sound better than upgrading your 6x9s, as far as lows are concerned. However, upgrading your 6x9s and amping your existing speakers would also sound better than what you have. (and could probably be done a bit cheaper than a sub/amp/box setup).