What’s the best way to format ACF number fields for display on the front end?

You need to use the wp_footer action hook, similar to this

add_action('wp_footer', 'add_my_script'); 
function add_my_script() {
?>
<script>
// your script code here
</script>
<?php
return;
}

This hook will hook into the themes’ wp_footer() call, so it will happen as part of the theme’s display of the footer.

Place this code in the functions.php file of your Child Theme.

Read more about how the footer is displayed, and how you can modify it here: https://codex.wordpress.org/Plugin_API/Action_Reference/wp_footer

Added

Here’s is your script code inserted into my example. Syntax checks OK; I have not checked for desired operation.

 add_action('wp_footer', 'add_my_script'); 

function add_my_script() {
?>

<script>

 jQuery(document).ready(function( $ ){
 // Your code in here

 $( ".priceToFormat" ).each(function( ) {
 $(this).formatCurrency();
 }
 );

 $( ".numberToFormat" ).each(function( ) {
 $(this).text( $(this).text().replace(/(\d)(?=(\d\d\d)+(?!\d))/g, "$1,") );
 //$(this).toNumber();
 }
 );

 });

 </script>

<?php
return;
}

(Not sure why a downvote on my original answer.)