I have a geoJSON database with lots of polygons (census tracts specifically) and I have lots of long,lat points.
I am hoping that there would exist an efficient Python c
One cannot have really fast geometric code in Python. Instead the usual approach is to use fast C/C++ library with Python wrappers.
For example, you can start with CGAL - a very comprehensive C++ geometric library. It has Python bindings for most of its routines, see the link http://code.google.com/p/cgal-bindings/.