jQuery on Underscores menu

You haven’t passed jquery as a dependency for your script, and you are using the dollar sign too, which is not directly supported in WordPress due to conflict.

First, pass jQuery as a requirement while enqueuing your navigation.js:

wp_enqueue_script( 
    'themename-navigation', 
    get_template_directory_uri() . '/js/navigation.js', 
    array('jquery'), 
    '20151215', 
    true 
);

Then, wrap your code in a self invoking function:

(function($){
    // You have access to $ here
})(jQuery);

Or even better, define the $:

var $ = jQuery.noConflict();

$('body').click(function() {
    alert("Yeah!");
});

Done.