Al-Qunut in the Witr Prayer is Sunnah
Question :
Some of the Imams continuously make the supplication of Al-Qunut in the Witr prayer every night. Has this been reported from our Salaf?
Answer:
There is no harm in that. Rather, it is Sunnah, because when the Prophet taught Al-Hasan bin 'Ali Al-Qunut for the Witr prayer, he did not order him to leave it off sometimes and not to always say it. This proves that both matters are permissible. For this reason it is confirmed from Ubayy bin Ka'b that when he would lead the Companions in prayer in the Masjid of the Messenger of Allah, he would leave off Al-Qunut some nights. This was probably so that he could teach the people that it was not obligatory. And Allâh is the Giver of success.
Source:
Ash-Shaykh Ibn Baz
Fatawa Islamiyah, Vol. 3 Page 322