There isn't an easy way, as far as I know, to do it directly on the iPad, as the iBooks app doesn't allow you to transfer PDFs to another app. You could open each PDF individually, email it to yourself via the 'share' icon (the icon of the box with the arrow coming out of it towards the top left), and then use 'open in' in Mail to open it in GoodReader - but if there are a lot of them then that will be time-consuming. Or you copy them to GoodReader via your computer's iTunes via file sharing : http://support.apple.com/kb/ht4094
Even though they aren't iTunes purchases, you should be able to copy them from iBooks over to the Books section of your computer's iTunes library via File > Devices > Transfer Purchases, and you can then find where they are stored on your PC by right-clicking one of them in the Books part of your library and selecting 'show in explorer' on the popup - that will tell you where they are stored so that you can add them to GoodReader via 'file sharing'.
I don't know about the other app, but if you can't copy them directly from that app to GoodReader then you might be able to copy them off the iPad via file sharing, and then add them to GoodReader