First, Bose speakers are a non-standard impedance, usually running around 1 to 2 Ohms (versus the standard 4 Ohm aftermarket speaker impedance). If you run 4 Ohm speakers with the existing Bose amp, the performance will be reduced due to the impedance mismatch. I believe that Crutchfield.com has a few low impedance speakers that may work well with your Bose system. You can also get replacement Bose speakers on eBay.
I am not a fan of Bose systems, so I replaced my entire Bose system with an aftermarket system, and added a real subwoofer between my second row captain's chairs, and I am very happy with it.