‘Have’ is more common. But ‘Has’ doesn’t sound horrible. It would be interpreted by a native speaker as (A period of ) three years has passed, with the (a period of) being implied. More colloquial is: The last time I saw you was three years ago. The last time we saw each other was three years ago. Your phrasing gives the statement a somewhat dramatic tone.

Have

You should use have since the subject is plural