I guess that your query converted LEFT JOIN
as follows:
SELECT
i.ID
FROM item_tb i LEFT JOIN stocks_tb s ON i.ID = s.itemID
WHERE
i.coID = '". $_SESSION['coID'] ."'
AND i.isProduct = '1'
AND i.isBom = '0'
AND s.brID = '".$brId."'
AND s.itemID IS NULL;
and this is faster than your query.