Is it permissible to secretly receive a bonus and a salary increase from the questioner's Haram director, knowing that the director admitted to his action?

You should be patient, seek reward from Allah, and supplicate that Allah protects you from the evil of the unjust manager.

Regarding taking the raise and bonus without his knowledge: - If it is due to you according to the employment contract or labor law that conforms to Sharia, and the manager is preventing you from it, and you find no other way to obtain your right except by this means, then there is no objection to taking the amount of your right without exceeding it. This falls under the issue of securing one's right. - If it is not due to you according to the contract, then you are not permitted to take anything, and you must endure the injustice until relief comes from Allah.