Since you're already extending another HttpApplication-derived class, my thoughts are to just copy the relevant source code from the NinjectHttpApplication class into your extended HttpApplication class. Rather than cut and paste it, just look at the source for NinjectHttpApplication in the Ninject2 Ninject.Web.Mvc extension project here.
I would specifically copy the stuff in Application_Start() and Application_Stop() methods. The other methods for registering controllers are nice, but you can register your controllers however you wish. You'll note in the Application_Start(), the kernel is created by calling the pure virtual function CreateKernel() -- you can simply create your kernel inline right there. Additionally, note the presence of the Kernel property on the NinjectHttpApplication class -- I'd copy that into your own class as well. It would appear the intent here is that the HttpApplication-derived class effectively serves as the KernelContainer.
Disclaimer: I haven't tried this to see if it works, though I will be shortly. I've used Ninject 1.x in a web project and intend to upgrade to Ninject 2 in the near future; however, I'll probably be able to derive directly from NinjectHtppApplication. Good luck!