An alternative to using canonical tags is to implement a rel="canonical" HTTP header.
This is the implementation approach that you need to take to specify a canonical URL for PDFs or other non-HTML documents.
You need to be able to access your site's .htaccess file to implement this and can specify a canonical URL using the following code:
<Files "file-to-canonicalize.pdf">
Header add Link "< http://www.website.com/canonical-page/>; rel=\"canonical\""
</Files>