First, as a general note, while it can be done, I always recommend that you never rename or delete an application if there are any models associated with it that have been added to your database.
(See this other thread for more details: Official CLI's command to rename an app)
Now, beyond that, our pattern is that we have a “project app” that serves as the project-specific location for entities that don’t belong to any more specific app. That includes management commands. (Side note: I’ve got at least four Django projects in production that never render web pages. They only exist to run management commands, and those management commands exist in that project-app directory.)