This, of course, is a matter of personal opinion. There must be at least a half-dozen of Shakespeare's sonnets that could be chosen by different people as his best. At the same time, there are many that probably wouldn't be chosen at all because they don't contain any especially brilliant concepts or images, or because they don't seem especially sincere. At the present time I am enamoured with his sonnet #55, which begins with the lines
Not marble, nor the gilded monuments
Of princes, will outlive this powerful rhyme;
But you shall shine more bright in these contents
Than unswept stone, besmear'd with sluttish time.
That fourth line amazes me. He is comparing a neglected marble headstone to a step in front of a house which a sluttish housemaid had not swept and scrubbed properly but only sloshed off with a wet mop, smearing the white stone a greenish brown composed of mud and horse manure. It was one of Shakespeare's outstanding characteristics that he used familiar, commonplace imagery and not the highfalutin metaphors and similes cribbed from Greek and Latin authors that some of his contemporaries affected.
But I used to think that Shakespeare's best sonnet was #73, which begins with the lines
That time of year thou mayst in me behold
When yellow leaves, or none, or few, do hang
Upon those boughs which shake against the cold,
Bare ruin'd choirs, where late the sweet birds sang.
Notice the conceit that the boughs are shaking because they are cold and not because they are being shaken by the wind. This one contains a dazzling display of metaphors and even metaphors within metaphors--all of them drawn from familiar, commonplace sources. In the first four lines, for instance, the speaker's time of life is compared to trees in late fall or early winter, and then the trees are compared, if I am not mistaken, to a choir in a ruined church (the choir being that part of the church used by an organized company of singers performing church music). The three stanzas in the sonnet each contain a metaphor and a metaphor within the metaphor.
On the other hand, Shakespeare sometimes uses a single striking and surprising metaphor, "like the dyer's hand" in Sonnet 111. Perhaps the best example is in his famous Sonnet 129, in which he says that lust is
Enjoy'd no sooner, but despised straight;
Past reason hunted; and no sooner had,
Past reason hated, as a swallow'd bait,
On purpose laid to make the taker mad:
I would have to say that in my humble opinion Shakespeare's most perfect sonnet is his sonnet #73, and the one that most deserves to be carefully studied.