The taxonomy of Galapagos Tortoises has been through many changes (and likely will continue to be). Geochelone nigra as used at this zoo is one of the "lumped" names for the species/complex, although Geochelone is now generally replaced with Chelonoidis. It's not "wrong" as such, it's just not the generally accepted current name.
In terms of which species the tortoises at Ueno are, if the complex is split into multiple species rather than one: Genetic Origin of the Two Galápagos Tortoises in the Ueno Zoo, Japan Based on Mitochondrial DNA Sequences
"We examined the genetic identities of two giant tortoises in Ueno Zoo, Japan. The mitochondrial genotype of the older tortoise, Taro, as appeared to be that of Chelonoidis porteri from Santa Cruz island. The mitochondrial genotype of the younger tortoise, Kamekichi, was identified as either C. becki from the northern area of Isabela island, or C. darwini from Santiago island."
