Yes, VLC can create a permanently cropped video.
The tutorial "How to crop video using VLC media player" on steemit discusses the method.
It's not simple though. You need to set cropadd filter preferences, which you'll have to manually calculate, and then use VLC's Convert/Save menu item to record a new version of the video with those cropped settings.
I did this once. It wasn't entirely intuitive (especially trying to figure out what values needed to be set under cropadd), but it worked well.
Depending on your patience, however, it might be simpler to locate a different program that is more simply used for this purpose.