This is the set I'm looking at. The sticker price on Amazon (through TigerDirect) is a little lower, but Samsung has free shipping which makes it about $50 less through Samsung. If Amazon stocked it directly I'd probably get it through them, even though I'd have to pay tax.
The Samsung site looks like the better deal? Go for it! Buying from the manufacturer should be fine? The only question I would have is what happens if there is a problem? Manufacturers generally don't like dealing with problems/customers. They prefer that to be Amazon or Best Buy's problem. That would be my only reservation.