snapcraft [options] register <snap-name> [--private]
Similarly, when registering a name in the store, you get a choice of making it private:
IIUC, this is orthogonal to a snap being published, and thought that the snap would be available to me and collaborators when published private.
You can also make the snap private at any time:
There's some snapcraft commands missing to do this, also it's impossible to change once you registered, but before you published - I'll file issues as appropriate.