Hello bindu,
We cannot say which is best among autonomous or affliated because it depends on various factors like infrastructure,placements....etc
But in autonomous there will be a little own rules and more pressure on students.
Hope this answer helps you,
Goodluck,
Thankyou.

Dear there is nothing like which is best.It depends on various factors like infrastructure, faculty, facilities etc.But in general you can expect that autonomous colleges are better than affiliated because the autonomous colleges have right to prepare exam and checked by the faculty of college.So,this leads to a fair marking and also an autonomous Institute is made when AICTE thinks it is capable.
Hope this clears your doubt.