I still don't have ePubs in my iTunes, but it doesn't look like we really need it.
On the Mac, make sure iCloud Drive is enabled and that you have iBooks selected in System Prefs->iCloud->iCloud Drive.
Do the same on the the iPad/iPhone, in Settings->iCloud->iCloud Drive.
On the iPad, in iBooks, there's a menu at the top that lets you view Collections. By default it has "All books", "Books", "Audiobooks", and "PDFs". At the bottom of that menu is an option to "Hide iCloud books". Uncheck that and you should have access to all your ePubs.