Yes, you can change the subwoofer, but as long as you follow a few important guidelines.
1) make sure that your new subwoofer is the same impedance as the old one to ensure that the amplifier is neither overloaded or overworked.
2) Make sure that the power rating of the new subwoofer is comparable to the old one. You don`t want a 500W sub when the amp only kicks out a few, otherwise at full volume, the amp will not even be tickling the sub.
3) Make sure that the size of the box you put the subwoofer in is the correct capacity for the subwoofer - as an incorrect sized box can sound worse, even with the increase in speaker size.
4) Remember that the BOSE sub and box was as good as they could make it and gives a balanced sound as many people will agree with. The sub is not too overpowering and adds a correct degree of richness and depth to the sound. Altering the sub will upset this balance.
5) If you do not like the BOSE sound, (and opinion is certainly divided on the forum) your best option is to rip out the entire system, speakers, amps, wiring and all, and sell it to pay for a decent sounding system - personally I cannot stand the BOSE system, but then I have been spoilt by the absolute cream of what is available.
8-)