I don't think it's the Great Deku Tree.

[DragonEleven]

But does he know if it's Ganondorf Ganon? That would be a much bigger detail that Link would need to know. The reason I say this is because tagging Ganon with the precursory name 'Calamity' along with referring to him as 'it' makes it sound way too much like it might be some other Ganon-like creature (potentially risking confusing Link, just in case Link did still remember any stuff about Ganondorf) and not Ganon himself.

Apparently the original Japanese only referred to him as 'Ganon'... the 'Calamity' part seems to be a result of the localisation teams getting creative... the original line was probably translated to 'the calamity known as Ganon', then they shortened it to 'the calamity, Ganon', which they probably liked the sound of, so they went with 'the Calamity Ganon' instead (this isn't the first time the localisation team has caused confusion by messing with names, and probably won't be the last).

So this is 'Ganon' and the only 'Ganon' there has ever been was once Ganondorf, so I expect this will be brought up at some point during BotW (possibly with the Gerudo), but it is not something that Link would have needed to know about at the very start of the game, which is all we've really seen at the moment.