Well, of course. It is canon and will never not be since as much as we'd like to be, NMA is not in charge of what is or what is not canon within the Fallout universe. Bethesda is.
Whether it should however is up to debate. Personally, I have to give props to Bethesda for keeping their hands off of the Core Region/West Coast and making their own distinctive Fallout setting on the East Coast. In that regard, it makes a nice and easy continuity split. To me, Fallout 3 and 4 are in their own little continuity on the East Coast. They have their own tone, style lore and that's their thing. They do how they do. Similarly, Fallout 1,2 and New Vegas are in the other contiunity with their own tone and style. Tactics is the semi-canon border zone that both sides pick from.
Unfortunately, aspects of Fallout 3 HAVE to be canonized as they are directly referenced in New Vegas. i.e Adams Air-Force Base, General Autumn, the Hellfire Armor. There's also reference to a splinter group of the Brotherhood out East but that's vague enough that you can come to your own conclusions.