It is possible that the singular/plural choice is not a purely syntactical matter, but partially depends on whether the speaker's focus. The second and third examples are both correct. Which one is the best is obviously a question format, so it makes sense that which one the best is should be the correct form.
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I have two assignments, one of them is done. The first example is incorrect. I have two assignments, one of which is done.
Which one is grammatically correct or better?
Which one you use is mostly a matter of preference, although a hundred.