Manually create an order with a product ID woocommerce

I think you can use the following:

$order->update_meta_data( 'YOUR_META_KEY_HERE', $note );

Remember to replace YOUR_META_KEY_HERE with your preferred key,
Complete code:

add_action( 'gform_after_submission_56', 'post_to_third_party', 10, 2 );
function post_to_third_party( $entry, $form ) {
    global $woocommerce;
    // use this to find out $entry output
    var_dump($entry);

    // Make sure to add hidden field somewhere in the form with product id and define it here, If you have some other way of defining products in the form you need to make sure product id is returned in the variable below somehow
    $user_id =rgar( $entry, '97' );
    $note = rgar( $entry, '53' );

    $product_id = rgar( $entry, '71' );
    $quantity = rgar( $entry, '73' );


    $address = array(

         'first_name' => rgar( $entry, '98' ),
         'last_name'  => rgar( $entry, '99' ),
         'company'    => rgar( $entry, '' ),
         'email'      => rgar( $entry, '83' ),
         'phone'      => rgar( $entry, '84' ),
         'address_1'  => rgar( $entry, '88.1' ),
         'address_2'  => rgar( $entry, '88.2' ),
         'city'       => rgar( $entry, '88.3' ),
         'state'      => rgar( $entry, '88.4' ),
         'postcode'   => rgar( $entry, '88.5' ),
         'country'    => rgar( $entry, '88.6' ),

    );



    $order = wc_create_order();
    $order->set_customer_id( $user_id );

    $order->add_product( wc_get_product($product_id), $quantity, $prices); 
    $order->set_address( $address, 'billing' );
    $order->calculate_totals();
    $order->update_status("on hold", 'pending', TRUE);

    $order->update_meta_data( 'YOUR_META_KEY_HERE', $note );

}

Thank You