Academies cost 2 upkeep. So academy + generator = 3 sci while 2 arrays = 2 sci 2 energy. It really depends on the circumstances. There is a tech that provides the array with an additional +1 tech. There's also the virtue that provides the academy upgrade. That said, I also think that academies are probably the best improvement in the game.
I personally don't find terrascapes all that great. If they worked as advertised and provided +2/+2/+2 they'd be awesome, but all they do is turn a tile into a mediocre 2/2/2 tile, for which you pay 6 energy per turn. That's rather excessive considering the amount of worker turns you put in. They're only useful if you choose the according virtue and the tile is turned into 3/3/3.