Square Enix replied to my email with the following:
We apologize for the inconvenience you have experienced. In regards to Nier Replicant's bonus pre-order content, this content can only be obtained from available retailers. Unfortunately, we are unable to provide the content or DLC codes for any purchases. You will need to contact the respective retailer (Best Buy) that you purchased the game from for any bonus content you should have received as this should have been received as a separate package/code.
Thank you,
Alfred
SQUARE ENIX Customer Support