It depends on the layers of your application. The fact that it's MVC doesn't matter. Do you have a data layer? If so, it goes there.
This is a little bit like asking where your queries would go in a WinForms app. Again, if this is a non-trivial app, you probably have a UI, maybe a service layer, a business logic layer, and a data layer. The data layer is where your queries go.
In an MVC app, the controller knows how to react to events in the view. In apps that I've worked on, the controller will make a call to the business logic layer, and the BLL will then connect to the data layer. This would be overkill in trivial apps, but I'm not sure how extensive your application is.
The BLL and DAL are your model. So, the short answer is:
The queries belong in the model, not the controller.