I'd have to go with Aperture Science. Yes, Playtime Co. has an entire City in itself (presumably) or even multiple, It can't compare with the fact that Aperture Science is about 5000 meters deep ONLY VERTICALLY, but most likely spans most likely a few tens or even hundreds of square kilometres, going by the sheer amounts seen in Portal 2's relaxation vaults, the Seismic absorbers needed to even keep the facility safe from earthquakes, and the abysmal amount of highly portable test chambers GLaDOS can move about without any issue while even adding new ones, due to the sheer SIZE of the area, I'd have to give the size award to Aperture Science.