I'm sure the bonuses will be the same regardless. The only difference is which vendor will get the exclusive gear. For us I'd say since Game & Gamestation are the only ones stocking (or allowed to stock?) the CE for preorder then either one or both of those will have the armour and assault rifle.
Personally I don't care. I almost never used any of the bonus DLC armour & weapons in ME2 and I doubt this will be any different.