How long do you have in Kakadu itself?
If this is your only day to explore Kakadu (other than the Jim Jim Twin Falls Tour) then after the jumping crocodile cruise I would head straight for the park. Once inside the park boundaries I would stop at Mamukala Wetlands, and then head to Ubirr and explore the rock art and scenery (maybe stay for sunset).
Or - if you have time to do Ubirr on another day, you could also visit Fogg Dam, Window on the Wetlands Visitor Centre (both located before jumping croc cruise), maybe stop at the Bark Hut for lunch then travel on to Jabiru stopping at Mamukala Wetlands and the Bowali Visitor Centre.
Food was better & cheaper there than at the just about anywhere else in Kakadu.
If you are heading to Katherine from Kakadu, don't miss Pine Creek Railway Resort for great food en route to Katherine
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