Both are good. You can not compare the entrance exam like this you can compare the colleges. 
If we check the ratings of the colleges then colleges under COMEDK like BMS college, Ramaiah Institute and RV college have outstanding ratings. 

It has good to have good options in your hand.

You can also take admission in private colleges of Maharashtra through JEE Main. 

You can check the top private colleges through MHT CET and COMEDK below

MHT CET

-Bharati Vidyapeeth Deemed University

-College of Engineering, Pune

-GH Raisoni College of Engineering, Nagpur

-Maharashtra Institute of Technology, Pune

-Veermata Jijabai Technological Institute, Mumbai

-Bhartiya Vidya Bhavans, Sardar Patel College of Engineering, Mumbai

To check the complete list you can refer below link

Top Private colleges through MHT CET

COMEDK

BMS College of Engineering, Bangalore

Ramaiah Institute of Technology, Bangalore

RV College of Engineering, Bangalore

PES University, Bangalore

Siddaganga Institute of Technology, Tumkur

To check the complete list you can refer below link

Top Engineering Colleges through COMEDK

Good Luck!!