hello, I am going to give you the order like best government medical college in Kerala than best medical college in Tamilnadu than best medical college in Karnataka and after that Chennai and Pune respectively. 

Colleges Of Kerala: Medical College Thiruvananthapuram, Government Medical College Hospital- Kottayaam, Governmant Medical College- Ernakulum, Government Medical College- Thrissur, Government Medical College Parppally Kollam, Periyaram Medical College, Government Medical College- Palakkad, Government Medical College Hospital- Manjeri, T.D Medical College Hospital, Government T.D Medical College- Vandanam, Government Medical College- Konni, Super Speciality Block Calicut Medical College Hospital, Government Medical College Entrance- Paripally, Government Medical College Mourtury- Khozikhode, Academic Block Government Medical College- Thrissur, Government Hemopathetic Medical College- Thiruvananthapuram,Government Medical College Hospital- Idukki, Government Ayurveda Medical College Hospital- Ernakulam, Government Dental College- Kozhikode,Forensic Medicine Block, Kottayam Medical College

COLLEGES OF TAMILNADU: Theni Government Medical College, Government Kilpauk Medical College, Kanyakumari Medical College, Governmnet Chengalpattu Medical College, K.A.P Visvanathanan Government Medical College- Thiruchapalli, Maduarai Medical College, Government Medical College Omandadrur- Chennai, Thanjavur Medical College, Government Mohan Kumarmangalam Medical College - salem, Government Vallore Medical College- vallore, Govt Siddha Medical College- Chennai, Mamannar maruthupandiyar govt Sivagangai Medical College - Sivaganga, Government Medical College- Dharmapuri, Madras Medical College - chennai, Govt Thiruvaluvar Medical College, Govt Medical College - Tuticorin, Coimbatore Medical College, Tirunelveli Medical College, Govt Medical College And Hospital- salem

Colleges Of Karnataka : Hassan Institute of Medical Science, Raichur Institute Of Medical Science - Raichur, Banglore Medical College And Research - Banglore, Koppal Institute of Medical Science - Bhayanagar, Mysore Medical College And Research Institute - Mandhya, KIMS OPD- Hubballi, Govt Medical College- Bengaluru, Belagavi Institute Of Medical Science - Belgaum, VIMS- Bellarri, DR B. R. Ambedkar Medical College- Bengaluru, Jawaharlal Nehru Medical College - Belgaum, Bidar Institute Of Medical Science- Bidar, Gadag Institute Of Medical Science- Mahasamudra, Govt Unani Medical College- Bengaluru, Jagadguru jayadeva Murugarajendra Medical College- Davanagre, SHIMOGA Institute Of Medical Science- Shivamogga, Government Medical College- Bidar, Gulbarga Institute Of Medical Science- Kalaburag.

Colleges Of Chennai: Govt Medical College Omandurar, Govt Kilpauk Medical College, Madras Medical College, Government Yoga And Naturopathy Medical College, Govt Siddha Medical College, Madras Medical College And Government General Hospital, Madras Medical Colleeg Of Nursing, ESIC Medical College and PGIMSR, Rajiv Gandhi Govt General Hospital, Govt Medical College Ground, Stanley Medical College.

COLLEGES OF PUNE: B J Govt Medical College, Armed Force Medical College, Smt Kashaibai Navale Medical College And General Hospital, Z V M Unani Medical College And Hospital, B J Medical Gents College, Dr D Y Patil College, Hospital & Research Centre.

Hope this will help you.      

Top Government Medical Colleges in Kerala
1. Government Medical College, Thiruvananthapuram
2. Government Medical College, Kozhikode
3. Government Medical College, Kottayam

Top Government Medical Colleges in Tamil Nadu
1. Madras Medical College, Chennai
2. Stanley Medical College, Chennai
3. Annamalai University, Annamalai
4. Coimbatore Medical College, Coimbatore

Top Government Medical Colleges in Karnataka
1. Bangalore Medical College and Research Centre
2. Mysore Medical College
3. Karnataka Institute of Medical Sciences, Hubli

Top Government Medical Colleges in Pune
1. AFMC, Pune
2. Savitribai Phule Pune University
3. BJ Government Medical College, Pune
4. Tilak Maharashtra Vidyapeeth, Pune