Can I assume this occurs on multiple different CD'*? Could possibly be a dirty lens, also a few other problems that may be a little more difficult to repair.
As for a replacement, the head unit makes no real difference. These were the same whether you have Bose, Monsoon or no amp at all. You should have the AM/FM/CD/Cassette. In 2004 they changed to black buttons from gray. In 2003 the AM/FM button changed to BAND. This only means the head unit will support the XM receiver (if installed). You won't have this receiver, but the head unit will otherwise work fine. You just won't see XM1 or XM2 as you cycle through band choices. Any BONNEVILLE head unit from 2000-2005 should be fine.
If you find one on eBay, be careful! Many people advertise radios that will fit the Bonneville and other vehicles (Montana, etc). The connector on the Bonneville is very unique. You must find a Bonneville radio. It has one connector for the antenna and one wide white connector for the radio. Other radios that have the same looking face have one antenna connector and two black connectors for the radio.
StingRay Bike w/cards in the spokes, Weeeeeee!