I've lived here ever since I came to Tokyo three years ago.

Literal

3 years ago [target-に] Tokyo [destination-へ] came [since-以来] here [location-に] lived [progressive-ている].

~て以来 ('ever since X') marks a point in the past from which a state has continued. The matrix clause 住んでいる ('is living' = has been living) uses ~ている to express a state that began at the 以来 point and continues to the present — this is one of the key uses of ~ている: ongoing state from a change-of-state verb.