How to implement javascript to the theme Bootstrap
Please set z-index to solve it.

.b-left-side__pointer {
  z-index: 1;
}


Also, I have some advices for your code.


make use of Drupal behaviors instead of $(document).read()
use jQuery.once() to prevent event binding multiple times, it would happen if your page contains ajax.
use jQuery.toggleClass() to simplify the complexity of logic.


(function ($, Drupal, window, document, undefined) {
    Drupal.behaviors.sub_theme = {
        attach: function(context, settings) {
            $(".b-container__left-side", context).once('b-left-side', function() {
                $(".b-left-side__pointer", this).click(function(){
                    $(this).toggleClass('show');
                });
            });
        }
    }

})(jQuery, Drupal, this, this.document);


You need to change your CSS and also class name on HTML. I can't give opinion with that due to lack of information of your requirement.