I'm not sure why this hasn't been covered yet, but I think the easiest way to get a PDF document into iBooks is to email it.
Here's what I do:
1. Insert the PDF into an email (as a file attachement) to myself and send.
2. Open the email on my iOS device.
3. Tap the PDF icon in the email which causes it to finish downloading.
4. When it's done, tap and hold the PDF to get various choices (depending on what apps you have installed) and select iBooks or anything else for that matter!
I hope this helps someone.