Thank you for this question Erik. The Euro Aristo project recommends using patronymic names (house names) rather than territorial names, in order to group members of a family together with the same name and make them more easily searchable. We also leave out particles such as von, zu, van, of, de...
In the case of Johann I would go with Kleve, as he was German (members of the French branch of the family would be Clèves). That is for basics, but the house name of the Cleves family is actually Mark (von der Mark, La Marck in French), themselves descendants of the Berg family if Wikipedia is correct.
You could also check this previous discussion (about more recent French Cleves): https://www.wikitree.com/g2g/346640/proper-lnab-for-members-of-the-cleves-family-
As you can see, it is hard to reach a concensus for this family.