Goodreader syncs over WiFi, iBooks can only sync when connected to the computer via iTunes (unless they fixed it). Goodreader will open virtually every media file type, iBooks not even close. Goodreader allows you to annotate, highlite, attach notes, bookmark, and outline files. iBooks allows you to read an iPub document.

I've used both apps, iBooks doesn't come close to offering the features in Goodreader.