The best time to apply is 9 months prior to the commencement of your first semester.
For example, if you wish to join the University for the Semester beginning in September 2015, you should apply in December 2014 or latest by January 2015.
Most of the university offices are filled with white people who don't understand the Indian education system and take quite some time to process your application.
Continuing with the above example of September 2015 beginning semester, you should clear all your qualifying entrance tests like GRE and TOEFL by April of 2015.
Most of your critical documentation should reach the university admission office by March or April latest!
You should not have any problems applying and being accepted unless you are a student from Andhra or Telangana who is forging most of his or her documentation!