The first section of this sonnet is actually very ironic, as the speaker comments on the way that his love for his mistress overpowers his other senses. It is his heart that governs his emotions, and helps him to overlook the many defects in her character that his senses are all too aware of. Consider how the poet introduces this theme through the sense of sight:
In faith, I do not love thee with mine eyes,
For they in thee a thousand errors note;
But 'tis my heart that loves what they despise,
Who in despite of view is pleased to dote...
The speaker therefore does not love his mistress with his eyes alone, because actually they reveal a "thousand errors" in her appearance. It is his heart that is the organ of love which causes him to love her in spite of the many blemishes in her appearance.
As the poem continues, it becomes clear that it is the heart that has transformed the speaker into the "vassal" and slave of his mistress, even though she uses this to abuse him and cause him pain. The only advantage of the speaker's situation, as he ironically concludes in the rhyming couplet of the sonnet, is that it is the mistress who decides on how he will be punished rather than anybody else:
Only my plague thus far I count my gain,
That she that makes me sin awards me pain.
So, this sonnet begins by exploring the nature of love and how it overpowers our reason and other senses, before concluding with a rather grim and ironic closing showing the complete helpless devotion of the speaker to his mistress, even though she causes him pain and he compares his love-lost situation to having the plague.