Autonomus colleges under VTU are better. These colleges shave the autonomy to frame their syllabus, academic calender, curriculum, and evaluation methods. In comparison to VTU, you can score better. The overall learning experience is better.
RVCE, MS Ramaiah Institute of Technology, and BMS College of Engineering are among the most reputed autonomous colleges under VTU.
Autonomous colleges are the ones that are affiliated with VTU but have their own syllabus and conduct their own examinations. The degree will be awarded by VTU. Other colleges follow the VTU syllabus and examination.
Usually getting admission to autonomous colleges can be difficult, if your academic record is average. But assuming you are eligible for both options, you should know that both have their advantages and disadvantages.
However, placement after your degree depends on the institute, whether autonomous or not, you will get the same degree. So, the choice is entirely up to you.