Keeping in mind it's been years since I last went to Cologne, I have to give this to Berlin. There's three places in mind when I think of "African Animals in Berlin" - the Hippo house, the Giraffe house and the largest exhibit of that one section over the bridge. Berlin's hippo house is one of the best I've ever seen and, whilst Cologne's certainly isn't bad, I do like Berlin's better. I know Cologne doesn't have the giraffe house anymore, but even when it did, I just liked Berlin's better, combined with the novelty of a European rarity in the Southern Gerenuk. Finally, that exhibit over the bridge is a nice little take on the African Savannah mixed exhibit, including comparatively rare Springboks. Add on other factors like the bird collection (a reminder that about 1/4 of the Bird House is dedicated to African wildlife) and Berlin pretty much takes it.
Cologne definitely isn't without its merits, though. Its ape house is superior to Berlin's, and with both Bonobos and Western Gorillas, that's a key point. So, I'm gonna say 3/2 for now.