The easiest way to do it would be to use .htaccess at the public_html level.

You could either "deny from *" which will give a "forbidden" message to anyone that tries to visit the site.

Or, you could password protect public_html using cPanel would be another way to do it.

In either case, anything lower than public_html will follow the rules of the highest level .htaccess file.

You could also simply chmod 000 public_html which would do basically the same thing as a deny from all in .htaccess.