There will be slight differences in the drives supplied with the computers. Might not be issues at all, dunno. I'd put the old drive in the new computer's second slot and copy then remove the drive and replace it with a new one.
But the Apple migration assistant is a no-brainer and flawlessly brings over about 98% of your stuff form the previous machine. It's very cool.
This is my standard sigfile so do not take it personally: "For crying out loud, read the freakin' manual."