It really depends on the application and area of study. There is no "one best" language for all of scientific computing. For some things R is the best, for others SPSS, and for some matlab. The larger the datasets and the more computationally intense the task, the more low-level languages like C++ or Fortran are best.

But across subfields and concentrations Python is almost always the second best language. Also Python kills for rapid prototyping and testing a concept on a small scale before the much more labor intensive porting to a lower-level language.