cpyext is mature enough (numpy, cython, scipy, pandas soon) to support pythonnet in pypy. In fact pypy used to have a branch which ran on top of CLR (similar to IronPython), but this branch is not maintained.

The use of pypy in .NET is quite popular request:

http://stackoverflow.com/questions/6084697/is-it-possible-to-embed-pypy-into-a-net-application

The only limitation of pypy is 32-bit on Windows and poor support for Python 3+, although the latter is improving with funding from Mozilla.

Also this might be quite nice collaboration with pypy developers due to their level of expertise in python C-API and cffi.