subclassing UIWindow while using storyboards

UIWindow in a Storyboard project can be subclassed as explained in Apple’s UIApplicationDelegate reference:

window
When a storyboard is being used, the application must present the
storyboard by adding it to a window and putting that window on-screen.
The application queries this property for the window. The retained
reference to the window by this property is necessary to keep the
window from being released. If the value of the property is nil (the
default), the application creates a generic instance of UIWindow and
assign it to this property for the delegate to reference. You may
implement the getter method of this protocol to provide the
application with a different window.

In other words in your AppDelegate implementation simply add the following getter

Objective-C

- (MyCustomWindow *)window
{    
    static MyCustomWindow *customWindow = nil;
    if (!customWindow) customWindow = [[MyCustomWindow alloc] initWithFrame:[[UIScreen mainScreen] bounds]];
    return customWindow;
}

Swift

var customWindow: MyCustomWindow?    
var window: UIWindow? {
    get {
        customWindow = customWindow ?? MyCustomWindow(frame: UIScreen.mainScreen().bounds)
        return customWindow
    }
    set { }
}