Should the fallout dlcs for fallout 3 and New Vegas be considered canon to the fallout series?

They are part of the same game with same main character aren't they? So yes.

Why wouldn't they?

I think so. The way NV's DLC hook into the vanilla story, I find it hard to argue otherwise. Especially with the DLC characters being mentioned in the vanilla (Dean Domino, Elijah, Graham, Ulysses) and vanilla characters being mentioned in the DLC (House, Caesar, Veronica, Lanius) it would be odd to consider these expansions as non-canon.

Of course the main reason some people might believe they're non-canon is their hatred of Mothership Zeta. Yet with Broken Steel being a continuation of FO3's storyline and The Pitt providing history about the BoS's road to DC it's clear they are intended to fit into the canon story, Mothership Zeta included.