How to use entityform and ajax_form_entity in a modal window?
There is a sandbox module called Modal Entity Forms https://drupal.org/sandbox/andreymaximov/2058521

It depends on the Modal Forms module and will work in the same way, but for entity forms. I have tested the module and it works fine for now, although I want to submit 1 or 2 patches to extend it's functionality.

EDIT:
There is now a new module called Modal operations: https://www.drupal.org/project/modal
It's currently dev only (still better than sandbox) and so far it seems to work fine.