There are many possibilities.. if you haven`t visited the other dutch zoos, I´d go back to the Netherlands/Belgium. You could easily do Rotterdam Zoo, Safari Beekse Bergen and Antwerp in 3 days, Rotterdam and Beekse Bergen are among my all-time top favourites (together with Apenheul, but you`ve already seen that). Amersfoort and the dolphinarium Harderwijk aren`t far from Rotterdam neither, so there are many things to see zoo-wise.
Cologne combined with some of the zoos Toddy suggested would be nice too.
Or what about Basle/Zurich/Mulhouse?
Or Munich/Nuremberg/Augsburg? Munich and Nuremberg are great zoos, I havn`t seen Augsburg though. Munich is a fantastic city, too. Munich could also be combined with the Alpenzoo Insbruck and or the zoo in Salzburg.
More ideas: Leipzig/Dresden/Halle; Dresden/Prague/Usti nad Labem, Barcelona/ Bioparc Valencia/ Aquarium Valencia/ Tera Natura Benidorm, Hannover/Hagenbeck Hamburg/Osnabrück, or Leipzig/ Berlin Zoo/Berlin Tierpark!