My mother now wants to start Skyping Zac. Unfortunately, my wife does not really care about what Zac believes or if he wants to be a JW. So my mother rings her when I am not around and uses her to speak to Zac. No matter what I say to Mum, I know she will still go behind my back to try to indoctrinate Zac.
Sounds like your wife doesn't have your back on this 100%. So if you can't supervise the Skype visits personally, then you have to tell Mum point blank, "religious discussions of any kind (not just JW) are not allowed when 'visiting' with Zac. If I find out that you have not respected my wishes, then the 'visits' will end and you will not be permitted to Skype Zac, except in my presence".
Like others have said, you're the parent. You call the shots on what your child is taught or who they associate with.
Just remember, no matter how accomodating you may think you're trying to be, any perceived interference in limiting your mom's influence will be seen as persecution in her eyes and she will become a drama queen over it. That's where you have to set the boundry, don't back down, and put it in her court. Respect my wishes, everything's cool. Push me and I'll pull the plug completely and you'll lose all privileges.