Setting properties on the window object is equivalent to creating global variables. That is, sometimes doing it is inevitable, but you should try to keep it to a bare minimum, as it ends up polluting the global namespace.
In your case, creating a single property is not so bad. If you want to be extra careful about it, you can explicitly create a namespace for any stuff you need global access to:
// In init:
var mynamespace = {};
. . .
// Once the controller is available:
var namespace = window.mynamespace;
namespace.controller = controller;
namespace.foo = bar; // Set other stuff here as well.