Which is a better speaker to replace the stock Bose in my 2005? I only want to make this investment once so looking for a quality speaker.

Depending on what speaker I go with, I was told the car does have factory amps? Are these any good our should I buy new one? If so what is a good amp? I don't want anything super big. Just enough to do what it needs to. :p

I think you would be happy with both. If it were left up to me, I'd go with the focals. I've used focals before and they sound really nice to me. I have not used bostons personally, but they are a reputible company with good products and customer feedback.

As for amps, you will def. need to have an aftermarket amp installed to run them. The factory amp is not gonna work. If you're also replacing the smaller speakers in the rear, then get a 4 channel amp to run them. Alpine amps come to mind because of the quality and are relatively small size for the performace. Another thing to keep in mind when installing components in your doors is that you will need a set of door speaker adapters like ours listed in the link below. This is mainly due to the odd shape of the size and shape of the factory speaker opening. And having the adapters makes really simplifies the task of installing your front component set.
C5 Door Adapters (http://www.subthump.com/vetteaccy.htm)

Btw, no audio system is complete without a sub. I highly recommend at least a 10" in the back. You will never regret it.

Bouston Acoustics! Focals I know are high end speakers also. I have a friend who has nothing but Boustons in his SUV and that thing sounds great!