Bethesda let Obsidian make the game, so obviously they will consider it canon. Obsidian will also obviously consider it canon. But we wont know what ending is considered canon until the game Obsidian makes next, if they do. But that game will likely come after Fallout 4, so we may just find out something about the ending in Fallout 4 anyway.
This, basically. While anything that is not effected by player choice, ie: place names, people, background story exposition, etc... will only risk not being considered canon by direct contradiction in later releases, all issues related to player choice will not be fully canon until a later game shows which of those choices the devs have incorporated into the story. If no other Fallout game mentions anything at all about how things turn out in NV, then none of the possible main paths can be considered canon.