My vote is a tie between Let It Be and Here, There, and Everywhere.
LIB is a beautiful song. It has a beautiful message and I consider these lyrics to be his best ever, including anything in his solo career (of course!).
HT&E is just one of those little maudlin-type songs that works perfect for Paul. His voice and the melody are so affecting for me. I adore both of these songs by him. They are, together, my favorite song by Paul. And then Calico Skies and a few others would trail behind.
Oh, and I get sooooo annoyed by Hey Jude. I can't stand to hear it anymore. Its annoying and I don't think its one of his best, for me. But, hell, that is the beauty and art of being an individual- you got your own preferences for everything.