Praise be to Allaah.
How can your duaa (prayer, supplication) not be answered and not be of benefit to your son, when the Prophet (peace and blessings of Allaah be upon him) has said: There are three duaas which will undoubtedly be answered: the duaa of one who is oppressed, the duaa of a traveller, and the duaa of a parent for his child? (Reported by Ibn Maajah, 3852; see also Saheeh al-Jaami, no. 3033). The word parent [waalid, lit. father] includes both father and mother. You are his mother, who bore him, nursed him, fed him and brought him up. You are more compassionate towards him than all his other relatives, and you are the one who has suffered the most grief and distress because of his loss. Pray for him for forgiveness, mercy, Paradise and salvation from the Fire. Pray for him in your salaat and your sujood (prostration), in the last third of the night and on Fridays before sunset, and at all other times and in all other circumstances.
Be of good cheer and remember the great reward which will be yours if you bear this loss with patience, accept the will and decree of Allaah, and hope for reward. You have lost your child to One Who is more compassionate towards him than you, the Most Merciful, the Most Compassionate, Allaah, the Lord of the Worlds. You also have the consolation of knowing that if you and he die believing in Tawheed and in Islam, you will be reunited after death. The righteous will be reunited with their offspring in Paradise, even if they are of a lesser status than them. Allaah says (interpretation of the meaning): And those who believe and whose offspring follow them in Faith, - to them shall We join their offspring, and We shall not decrease the reward of their deeds in anything. Every person is a pledge for that which he has earned. [al-Toor 52:21]
As regards your question about what you can do for your father and your son who have passed away, you will find a detailed and comprehensive answer under # 763, which describes things which the living can do for the benefit of the dead.
Finally, we console you with the words with which the Prophet (peace and blessings of Allaah be upon him) consoled a mother whose son had died:
To Allaah belongs whatever He takes and whatever He gives. Everything has an appointed time with Him. Have patience and hope of a reward from Him. (Reported by al-Bukhaari, no. 6829). May Allaah bless our Prophet Muhammad.