I think you can do it with drupal_add_js(); it seems that the scope key option is your friend!
In your theme's
html.tpl.php there is a line
<?php print $scripts; ?>.
You can move it around anywhere you like, for example, place it after everything else, just before the closing
body tag to have all your scripts load at the bottom.
It's worth looking at using this module here to manage that for you https://drupal.org/project/advagg
I enabled AdvAgg Modifier and Advanced CSS/JS Aggregation. Then I visited settings page
/admin/config/development/performance/advagg/mod where I checked options:
Enable preprocess on all JS
Move all inline scripts to the bottom of the execution order
Move JS to the footer - All
And now I have all JS on the bottom (as Google recommends), without the need to change