New MacBook Pro: Migration Assistant or Time Capsule?

It actually doesn't matter. If you install Lion you can use the Time Machine backup as the source for restoring all data through Migration Assistant. It works exactly the same as if you put your old machine into target disk mode and use it as a drive for Migration Assistant.

(I was really surprised to find this out a couple of days ago when shuffling hard drives - 3 bad SSDs in a row, long story - and I was not allowed to select Time Machine to restore from because it was too large for the 240GB SSD, after using a 750GB spinning disk for a while - even though I had carefully excluded enough data to be sure it would fit. Then when Migration Assistant came up it allowed me to use the Time Machine drive to restore all the data I wanted anyway - all 90GB of it. All's well now, and this unexpected feature of Time Machine saved me some time.)