Configuring DI when using four-layer architecture
Actually, in this case you are not configuring ninject in presentation layer, as the presentation layer in case of MVC is cshtml files. 

DI engines (like ninject) should be generally configured in the start-up part of application, not in any specific layer. DI has nothing to do with logical decomposition of your application into layers. DI engines only role is to automatically 'distribute' dependencies to objects, usually by interfaces.
In case your application is modular and modules shouldn't see each other, than yes - in this case you probably need per-module DI set-up.

Coming back to ASP.NET MVC, in this case the initial object that are created are controllers and you need to provide implementations for it's dependencies (like you did in the code piece). Now if these dependencies - for exampl HomeService, have their own dependencies, these would need to be registered in the same ninject DI contaier right? So as you see, DI spawns across whole MVC application layers.