I've just finished this addon. It needs a few edits to work, but then it's fine for use. First of all edit the theme you use and add:
Change the hex color (#272822) to the one of the background (in settings, the main view background).
Now here's the addon:
Name the folder and file HighlightWhitespace and it should work fine. I don't know how to make a sublime-package file, if anyone does please tell me how so I can make one. (:
If it doesn't highlight (after restart) try to press ctrl+shift+W and it should work.
Hope it helps.
Managed to get the sublime-package. Here is the download: ckers.nl/sublime/HighlightWhites ... me-package
Just download the package and double click it and it will be installed. Remember: You still have to edit your theme with the code above!
Then restart Sublime and press ctrl+shift+w to activate.