You've got a couple of options, you can either just sync them to it by connecting the new iPad to your computer, selecting it on the left-hand sidebar (you can enable the sidebar via control-S if it's not showing), and then on the right-hand side of the iTunes screen use the Books tab to select and sync them to it :
If you have Settings > iBooks > Sync Bookmarks 'on' on both iPads it should copy your notes and highlights between them - from http://support.apple.com/kb/HT5557
Wirelessly sync your Bookmarks, Highlights, and Notes with your other devices using your iTunes Store account by tapping Settings > iBooks > Sync Bookmarks > ON.
Or you can try restoring the backup of your old iPad back onto it - now you have the PDFs on your computer's iTunes library it should be able to restore them onto the new iPad.
Backups and restores : http://support.apple.com/kb/HT4079