NO! No autoconf! It is better to use cmake. Like all KDE or rpcminer is using. I had in future plan to take care about it so you can assign me this task. Additionally QtCreator also support it.
The problem with qmake is that it is not intelligent enough to handle changes in library names (common with boost) and doesn't offer installation.
cmake, on the other hand, yes that might be a good choice because it can also generate native Visual C++ / XCode build files.
I'm not a that much of a fan of autotools either.
Mingw is generating libraries for Windows, so you can use without problem from VS in mingw or from mingw in VS.
You can link from mingw to C libraries compiled with Visual C. C++ doesn't work because it uses a different ABI. Or at least that used to be the case.