I have to develop an application for windows that will enable controlling the mouse through web cam by recognizing hand gestures. I will be using vc++ 2008 for development. But
If you are acquainted with Win32 API, then go Win32 API. It is the natural choice in your case since most of your source code will be video capturing, image processing, algorithms, and interfaces to mouse in Windows. When you are interested in performance, be closer to the hardware avoiding thick layers like .NET.
I believe that .NET is for complex business applications not for real-time applications or device drivers.