Witr prayer is a special prayer in Islam, and the best supplication (Dua) for it is Dua-e-Qunoot, which is recited in the last rak'ah of Witr prayer. Here is the English translation of the Dua:-
"O Allah! We seek Your help and ask for Your forgiveness. We believe in You and put our trust in You. We praise You in the best way. We thank You and are not ungrateful to You. We forsake and turn away from those who disobey You. O Allah! We worship You alone, offer prayers to You, and prostrate before You. We hasten towards You and serve You. We hope for Your mercy and fear Your punishment. Indeed, Your punishment will surely befall the disbelievers."