The Oxford English Dictionary gives the primary spelling as Epirot.

It gives Epirote as an alternative spelling, but this is muddied by a now-disused alternate definition from the 17th century of 'a person who lives inland.' (Epeiros means land or mainland).

So Epirote is acceptable, but Epirot is what is most used in modern English. It is also possible that different style guides for particular publications have their own rules on which to prefer.