To expand on @sir-muffington's comment to his own answer:
A similar error can occur due to corruption in the NTFS filesystem.
This happened in my case. Only I kept getting "input/output error", rather than "permission denied".
It happened when I hibernated with the NTFS drive mounted, and booted the Windows it belonged to. Some files got corrupted, and I couldn't remove them or their folder.
ntfsfix couldn't help. What helped, was booting Windows, right-clicking the drive in explorer and telling it to check it - fixed the problem in a matter of seconds.
So if you've got input/output errors(and they're not because your HDD is dying) - and ntfsfix isn't fixing them - it seems like using Windows' chkdsk is the only option. As it seems that no tools on Linux have the capability to properly repair NTFS. Alternatively, you can look to live tools like UBCD4win. It's ancient and might not even boot on modern devices, but it comes with an original chkdsk on it, and is only about 400MB.