WooCommerce - Get Newest Order ID By UserID and Product ID

gistfile1.php

<?php

global $wpdb;

$query = 'SELECT oinfo.ID
           FROM ' . $wpdb->base_prefix . 'woocommerce_order_items as oitem
          LEFT JOIN ' . $wpdb->base_prefix . 'posts as oinfo ON oinfo.ID = oitem.order_id
          LEFT JOIN ' . $wpdb->base_prefix . 'postmeta as ometa ON ometa.post_id = oinfo.ID AND ometa.meta_key = "_customer_user"
          LEFT JOIN ' . $wpdb->base_prefix . 'woocommerce_order_itemmeta as oimeta ON oimeta.order_item_id = oitem.order_item_id
                AND oimeta.meta_key = "_product_id"
                AND oimeta.meta_value = ' . $product_id . '
          WHERE ometa.meta_value=' . $user_id . ' ORDER BY oinfo.ID DESC';

Personally, I would write it this way. Table prefix is hard-coded, just because of laziness. :)

SELECT 
    ORDER_META.post_id AS order_id
FROM
    wp_postmeta ORDER_META
    JOIN
    woocommerce_order_items AS OI ON
        (OI.order_id = ORDER_META.post_id)
    JOIN
    wp_woocommerce_order_itemmeta AS OI_META ON
        (OI_META.order_item_id = OI.order_item_id) AND
        (OI_META.meta_key = '_product_id') AND
        (OI_META.meta_value = $product_id)
 WHERE
    (ORDER_META.meta_key = '_customer_user') AND
    (ORDER_META.meta_value = $user_id)
ORDER BY
    ORDER_META.post_ID DESC

Changes

• Removed one unnecessary JOIN
• Use INNER JOIN, rather than LEFT JOIN, as we don't need orders that don't match the criteria.

Not sure how I haven't seen your reply until now :) great optimization, when I've coded this it was mostly for internal use, so I didn't go for speed optimizations.
I personally love left joins because they still work if the database is damaged for some reason, and the results are null.