In Safari, tap on the PDF you are viewing to bring up a banner at the top with Open in on the left side and Open in iBooks on the right. Tap the latter and you will download the PDF to iBooks.
Create a folder (aka Collections)
If you begin to use iBooks to collect PDFs, you’ll eventually reach a point where you’ll want to bring some order to iBooks’s shelves. You can organize your PDFs into folders, which iBooks calls Collections.
To create a Collection, tap All Books at the top and then tap New Collection and give it a name. This new Collection will then get added to the list.
The current collection you are viewing is listed at the top of iBooks, which includes four default collections and any you created. In fact, one of the default collections is titled PDFs, which automatically pulls in any PDFs you save to iBooks.
Add PDFs to a Collection
To move a PDF to a collection, go to the All Books view where all of your files in iBook are listed and tap Select in the upper-right corner. Next, tap the PDFs you want to move and then tap Move in the upper-left corner. After tapping Move, you can then choose a destination for the files you selected.