Is it permissible to give charity on behalf of a disobedient son who prays negligently, knowing that he still receives his allowance from his father, and how can he be helped to find guidance?

You should advise your son to abandon his negligence in prayer and his sins. If he does not respond, then disavow his actions in your heart. And humbly supplicate to Allah, praying for his guidance and repentance, for a parent's supplication for their child is answered, as is authentically stated in the hadith: "Three supplications are answered without a doubt: the supplication of a parent for their child, the supplication of a traveler, and the supplication of the oppressed."