Put your version in the URI. One version of an API will not always support the types from another, so the argument that resources are merely migrated from one version to another is just plain wrong. It's not the same as switching format from XML to JSON. The types may not exist, or they may have changed semantically.
Versions are part of the resource address. You're routing from one API to another. It's not RESTful to hide addressing in the header.