Are there any controllers that are compatible with Antminers (specifically the s-9) such as a rasbperry pi?
I've only known the raspberry pi that are compatible with the Antminer and my friend is using it with his Antminer U3 why would you want other controller if you had known the raspberry pi? And if you are planning on running more than one Bitcoin miner at the same time, it is best to use a powered USB hub. Take into account the power rating as mining will need a lot of power, as much as one mp per miner.
I'm unsure what you just told him? what does a usb hub have to do with anything on the antminers???
As for controller, I believe the stock one CAN control 9? or was it 12? boards?
So you could basterdize them.
Maybe if the op gave a bit more info on what they are after out of this question?
As for directly plugging boards into a pi, No that's not possible.