I feel like the institute ending most likely was the canon ending primarily because shaun is the sole survivors son among other things, even though the institute is not exactly morally right (really only the railroad and the minutemen can come close to that moniker). I feel most people let feelings come before true morals and that includes their love for family, which means that the sole survivor would at the very least not destroy the institute even though shaun is a manipulative POS who only sees his father as a tool to accomplish a means to a cause.

If not the institute ending, then probably the minutemen or railroad endings would be canon, as the sole survivor definitely comes off as a person who would, without a doubt, try to keep doing the right thing heavily into consideration.