From what I understand, replacing a Bose system in a car is difficult for the DIY user.. Doesn't it have tweeters built into the dash? Also, is there not some like 6 channel amp somewhere, or something weird like that? If you can get a audio shop to replace the entire system that would be your best bet, because the speakers and tweeters are wired together and go to the amp before they go to the headunit, so you can't just replace the speakers because they would have different impedances.
And as for brands, there are many, but in car audio there are several higher end companies, many common brands can be found here at reasonable prices: http://www.sonicelectronix.com/
Some reputable brands I can recommend from experience are Polk, and JL Audio. Stay away from the cheaper products like Sony, and Jensen, if you care anything about a balanced sound quality. Kicker, Rockford Fosgate, and Apline are also brands to look at, but they cater to a more bassy Hip-Hop brand of people, they sound good in that genre as a result, but aren't balanced or advertised to be so.