With Bob Dylan considered one of the most important musicians in and after the 1960s, it's not surprising that trying to sort out the best Bob Dylan song is a popular tag.
Rolling Stone believes that "Like A Rolling Stone" is not only the best Bob Dylan song, it is the greatest song of all time. Given differences in taste, there likely will never be unanimity, particularly since Dylan has written and recorded hundreds of songs. Moreover, Dylan's evolution as a performer leads to plenty of debate and differing opinions.
Ultimately, the best Bob Dylan song is the one the individual listener likes the best.