I would say it's a judgement call on your behalf. Installers are either good or bad no matter where they choose to work. Ask around to some of the people you know that have had work done. A dedicated stereo shop usualy has a decent insyaller and in todays economoy they are priced pretty close to BB and CC. Don't always just ask for labor prices. A lot of the time best buy will offer "free" installs on their head units and then charge like double the normal price on the dash kit, wiring harness, and antenna adapter. So in the end you end up paying for the insall regardless of where the money was put on the invoice. So just get the whole picture before you make a decision
You won't get the service or expertise as a dedicated sound shop, but you also won't get the cost.
Of the two, I suggest Circuit City over Best Buy. The staff at Circuit City were more knowledgeable, more prompt, and over all better. The staff at Best buy (at least my local one) were morons. Circuit City has also been the best in most other areas. The only way that I have seen that Best Buy has beat Circuit City (at least in my area) is the variety of things like CDs and DVDs.