I concur with both “Paradoxurus” and “Batto” that, whilst in Paris, you should definitely see the Galerie de Paléontologie et d'Anatomie Comparée.
You should certainly visit the main natural history museum (La Grande Galerie de l’Evolution) too; of special note in this museum is the gallery of extinct and endangered species.
Others have mentioned elsewhere on ZooChat that this gallery includes the kouprey (which was at Vincennes Zoo in the 1930s) but, frustratingly, this specimen has never been on display on any of my visits. However, there are plenty of other interesting exhibits including a mounted quagga, blaubok and thylacine. (The blaubok is the highlight for me; the only other mounted blaubok that I have ever seen is in the one in the museum at Leiden.)
It is worth adding that both of these places are very close to the Jardin des Plantes Menagerie so, if time is limited, it would be very easy to see all three on one day.