"Not equal" is "<>" in SQL.
Try changing it to that and see what happens.
This should be your query:
SELECT *
FROM ProductMaster
WHERE CatalogId = 1007
AND SubCode LIKE '%A%'
OR SubCode LIKE '%B%'
AND EntryUser = 'Green'
AND ProductMasterId <> 1000
This is proper syntax and will work provided your logic is correct. Try removing one section of your where clause at a time and see where that gets you.