It is not permissible to ask Allah’s Messenger (peace and blessings be upon him) after his departing this world to seek forgiveness for one or pray for one. After passing from this world, the Prophet (peace and blessings be upon him) cannot affect any deed pertaining to this world. He is now experiencing a transitional kind of life in his grave, the truth about which is known only by Almighty Allah. As for the Qur’anic verse referred to in the question in hand, it is unanimously agreed among the righteous predecessors that it has to do with the lifetime of the Prophet (peace and blessings be upon him) only.  

Dr. Husam al-Din Ibn Musa `Afana, professor of Usul Al-Fiqh, Al-Quds University, Palestine states the following: It is not permissible for one (nowadays) to invoke Allah’s Messenger by saying “O Allah’s Messenger, seek forgiveness for me or pray for me,” whether this is said before the Prophet’s grave or elsewhere. Doing this—Allah forbid it—is a kind of shirk (associating other gods with Him Most High), for the Prophet (peace and blessings be upon him) has departed this world to the world of the Hereafter, the truth about which only Almighty Allah knows. Almighty Allah says, addressing the Prophet: (Lo! Thou wilt die, and lo! they will die) (Az-Zumar 39: 30).

The Prophet (peace and blessings be upon him), having passed away, cannot affect any deed relating to this world. With regard to the verse quoted in the question in hand, it has to do with the Prophet’s lifetime only.

Ibn Taymiyah, tackling a similar question, said: “(After the Prophet’s death) some people claimed that Almighty Allah’s words (If they had only, when they were unjust to themselves, come unto thee and asked Allah’s forgiveness, and the Messenger had asked forgiveness for them, they would have found Allah indeed Oft-Returning, Most Merciful) (An-Nisaa’ 4: 64) mean also that they can ask the Prophet (peace and blessings be upon him) after his death to seek Allah’s forgiveness for them; doing this, according to them, will be like asking the living companions to seek forgiveness for them.” Ibn Taimyah went on: “By claiming this, those people went against the unanimity of the companions themselves and those who followed in their footsteps as well as the rest of wise Muslims in this regard. None of those righteous predecessors was ever reported to have sought the intercession of the Prophet (peace and blessings be upon him) nor asked him for anything after his death. None of the eminent scholars has quoted something to this effect in their writings. It is only some recent (non-qualified scholars) who reported a false story about Malik (may Allah be pleased with him) in this regard.” (Magmu` Al-Fatawa, vol.1, p. 159)

The eminent scholar Muhammad ibn Saleh Al-`Uthaymeen said on tackling the different kinds of intercession: “The fourth kind of intercession is to seek the intercession of a person whose prayer is most likely to be accepted by Almighty Allah. An example of this is the Companions’ asking the Prophet (peace and blessings be upon him) during his lifetime to pray for them as in that case when a man entered the Prophet’s Mosque on Friday while he (peace and blessings be upon him) was delivering the Friday sermon and asked the Prophet to beseech Almighty Allah to cause it to rain to deliver them from drought. `Ukashah ibn Muhsan was also reported to have asked the Prophet (peace and blessings be upon him) to invoke Almighty Allah so that He Most High make `Ukashah one of those who will enter Paradise without being brought to account for their deeds. This is to be done during the intercessor’s lifetime. A person’s intercession cannot be sought after his death, for he cannot then affect any kind of worldly deeds. That was why when there was drought during the caliphate of `Umar (may Allah be pleased with them), the Muslims did not invoke the Prophet (peace and blessings be upon him) [who was dead then] to beseech Almighty Allah to cause it to rain. `Umar then asked Al-`Abass (the Prophet’s uncle) to pray to Almighty Allah for this purpose.

However, there is a false story related to the effect that a Bedouin stood at the Prophet’s grave and beseeched, “Peace be upon you, Allah’s Messenger. Almighty Allah says, (If they had only, when they were unjust to themselves, come unto thee and asked Allah’s forgiveness, and the Messenger had asked forgiveness for them, they would have found Allah indeed Oft-Returning, Most Merciful) (An-Nisaa’ 4: 64). Here have I come to you so that you may ask Almighty Allah to forgive my sins and intercede with Him for my sake.” This verse has no evidence at all for the claim that one may seek the intercession of the Prophet (peace and blessings be upon him) after his death. Besides, the verse tackles a situation about a certain group of people who did not want to resort in judgment to Almighty Allah and His Messenger (peace and blessings be upon him) as indicated from the preceding and following context of the verse.” (At-Tawasul, Ahkamuh, wa Aqsamuh, pp. 22-3)

To sum up, it is not permissible in the viewpoint of Islam that a Muslim (nowadays) asks the Prophet (peace and blessings be upon him) to seek Almighty Allah’s forgiveness for him or pray for him whether at the Prophet’s grave or elsewhere.