I think it's a largely irrelevant question. Canon is a malleable thing. Is Fallout 3 canon? At the moment, yes. The next one could come out and turn the whole thing on its head-- with a flat-out retcon if they wanted to be blunt about it, and with a subtle massaging of setting details if they wanted to be a bit more clever. I'm sure the average original-series fan would be happy with either at this point, just as I'm sure that neither is likely to happen unless Fallout 4 is the product of other minds than those that were behind 3. I'm just saying that canon isn't something to worry about unless you've got one that's close to pristine. In any other situation, there are going to be iterations of a series that you enjoy and iterations that you don't, but most of them are going to be just chockablock with things to pick at either way.
F3 is canon. I don't like it, but there it is. Practically speaking, it's probably not going to matter by the time F4 rolls around, because even if they don't change a thing the next game is only likely to touch on the events in the previous one in the blurriest of ways, and, like every other Fallout game (AND TES game, for that matter) the precise details of the hero's journeys in the former installments are largely going to go unmentioned.