Hmmm, there are two ways you can approach this I can think of, unless Kovid has a suggestion. Quite frankly the simplest way is to use a sledgehammer - close calibre, open your calibre configuration folder, delete the entire configuration folder (not just the plugins subfolder - the whole thing to include all your calibre preferences). It won't touch your library in any way, but it will mean you lose any tweaks, plugins, customised toolbars etc. Then Restart calibre, point to your library location, put back in your customised settings and reinstall the B&N and Goodreads plugin. That should *guarantee* no more issues.
Alternatively uninstall the Goodreads plugin and close calibre. Then go poking around in all the calibre configuration files looking for any occurrences of "Goodreads" and try to remove them from the file. However there is (1) a chance you will screw up and cause calibre errors, and (2) a chance that the file might be a pickle file which can't be edited in a text editor like a json/py file can. So you would end up having to delete the whole calibre configuration directory anyway.
Up to you, unless Kovid has any better ideas but the first suggestion above is the easiest. You can always copy any settings like tweak values, regexes etc to a text file to paste back in afterwards. Or take screenshots of your settings pages.