Is there a canonical outcome of the events in the Fallout 3 ending?

As far as I know, there is no canonical version of events (yet). Only two games take place after the events of Fallout 3:

• The Broken Steel add-on, which contains eventualities for both cases of the choice.

• Fallout: New Vegas, which takes place in a very distant location which should not be affected by that choice - in Fallout 3 it's stated pretty explicitly that the effects of the choice will take place in the Capital Wasteland, but no other region is mentioned.

Fallout 3 is the most recent-game in the series, chronologically, as far as the east coast is concerned, so at this point, it is unknown. While New Vegas takes place after the events of Fallout 3, the finale is not discussed, leaving things ambiguous.

Broken Steel (Fallout 3's DLC add-on which takes place after project purity) allows for either option.

In Fallout 4, Deacon mentions how "you can drink the water" in the Capital Wasteland, hinting at the Lone Wanderer's success in the activation of Project Purity.