Both can fit to be canon. One could make Goku & co have amnesia @ the end of super. GT was canon to the anime anyways, so there. You have your answer. Lol
I'd definitely pick GT over Super. I like some of the ideas, like Goku Black (before he was revealed to just be Zamasu in Goku's body), but it's still dookie on a stick to me, and the palette swaps are asinine.
Neither..... Sorry, I just cant pick one. Super has better fights and other things they do better than GT, but is still sub par, and GT is really no better IMO, so I vote for both to be non canon!
Probably Super, because it at least doesn't have the walking, massive plot hole known as Super 17, but both are contradictory as shit and overall crap.