There is no certain way of identifying the biblical "gopherwood" at this remove (translators took what would be a resistant tree wood in their area and applied the name to it). Some early works refer to a black wood. This may be hyperbole, suggesting ebony or an ironwood.
In English, the name ark for a boat seems to go back to the Lindisfarne Gospels, ca. 950 AD (ærce Noë). In the Jewish tales, the boat was covered, like a box or coffer; thus, "ark."