The best replacement for cython is pypy.

The best alternatives to cython are rated as following:
★★★★★  pypy
★★★★  ctypes
★★★  swig
★★★  numba
★★★  boost python
★★  numpy
★★  pyrex
★★  julia
★★  weave
★★  f2py
★  cffi
★  shedskin
★  jython

Your alternative for cython is not listed? Suggest!
Speaking about cython, one probably shouldn't forget about numpy.

Other search terms related to cython and their ratings are:
★★★★★ numpy
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