Mail may not have a Print PDF to iBooks button, but 3D Touch on iPhone 6s lets you do it anyway!
The ability to "print" iOS content to a PDF file was a long time coming. Even when Print PDF to iBooks was added to the Share Sheet, however, the built-in Mail app was left out. Because, of course, Mail still lacks the Share Sheet. If you have one of the iPhones 6s, though, you can work your way around that. All you need it 3D Touch.
How to print an email message to PDF on iPhone 6s
Again, this only works with 3D Touch, which means it currently on works with the iPhone 6s and iPhone 6s Plus. If you have either of those devices, you're good to go.
Launch Mail from your Home screen.
Open the message you want to print.
Tap on the Action button at the bottom. (The same one you'd use to reply or forward the message.)
Tap on Print.
Press firmly on the Thumbnail image to "peek" at it with 3D Touch.
Press firmly again to "pop" it into a full PDF preview.
Tap the Share button at the top right to bring up the Share Sheet.
Tap on the share or action extension you want to use to share or save the PDF.
You can save to iBooks right from there and, if you have the apps installed, to Dropbox, Google Drive, Kindle, and other storage providers. You can also share via Messages, Mail, and any other apps you have available, like Slack. You can even access your Workflow automations.
Can I print an email to PDF on older iPhones or on any iPad?
Not as yet, alas, though hopefully Apple will bring something akin to full-on Share Sheet functionality to Mail in the near future.