I've used Amazon for 2 or 3 Mac purchases and haven't had any problems. Their rebates are nice. 🙂
Buying from Apple, you're eligible for a $100 printer rebate, and in the very off chance your new Mac has a problem right when you receive it, they'll swap you out for a new one (assuming you didn't get a custom config). With Amazon, you'd have to wait for the new one to be shipped, then you'd have to ship the old one back.
I'd do whichever one is a better financial deal for you. 🙂