What should I do ME or MBA after B.E Biomedical Engineering???? Which one is good option for me???

It totally depends upon you, both M. E and MBA are good options after completing B.E Biomedical Engineering. You can choose one of these courses according to your interest and background.

I would suggest you to do M.E Biomedical engineering, as it is very much relevant to your background. Following are some good M.E Biomedical engineering colleges in India:

Amrita School of Engineering
Kasavanahalli, Carmelaram
Bangalore, Karnataka
(080) 28439565
(080) 28440092

Amrita Vishwa Vidyapeetham - Coimbatore Campus
Ettimadai Post
Coimbatore, Tamil Nadu
(0422) 2685000
(0422) 2656274

Bharath University
#173, Agharam Road Selaiyur,
Chennai, Tamil Nadu
(044) 22290742, 22290125, 22290247, 24404699
(044) 22293886

Indian Institute of Information Technology - IIIT Allahabad
Deoghat, Jhalwa
Allahabad, Uttar Pradesh
(0532) 2922000, 2922025, 2431684
(0532) 2430006, 2922222, 2431689

Indian Institute of Technology (BHU)
Banaras Hindu University,
Varanasi, Uttar Pradesh
(0542) 2368106, 2368427, 2307000, 6702078
9792262852, 9453788219
(0542) 2368283

Indian Institute of Technology - IIT Bombay
Powai
Mumbai, Maharashtra
(022) 25722545, 25767021
(022) 25723480

Indian Institute of Technology - IIT Hyderabad
Ordnance Factory Estate, Yeddumailaram
Hyderabad, Andhra Pradesh
(040) 23016033, 23016030, 23016026
(040) 23016032

Manipal Institute of Technology (MIT)
Manipal
Udupi, Karnataka
(0820) 2571060, 2925522
(0820) 2571071

Manipal University
Manipal.edu, Madhav Nagar
Manipal, Karnataka
(0820) 2922323, 2571081, 2922574, 2922530
9243777700, 9337789810

Motilal Nehru National Institute of Technology - NIT Allahabad
Teliar Ganj
Allahabad, Uttar Pradesh
(0532) 2545404, 2545407, 2545677, 2641520, 2641820, 2642865
(0532) 2545341

Narayana Engineering College
Narayana Avenue, Muthukur Road, A.K.Nagar
Nellore, Andhra Pradesh
(0861) 2313842, 2313843
(0861) 2341740

National Institute of Technology - NIT Rourkela Rourkela, Orissa
(0661) 2476773, 2462009, 2462031, 2472050
(0661) 2462999, 2472926, 2462022

S.R.M. University
S.R.M. Nagar Kattankulathur
Kanchipuram, Tamil Nadu
(044) 27417400, 27455510, 47437500
(044) 27453622

SASTRA University
Tirumalaisamudram
Thanjavur, Tamil Nadu
(04362) 264101, 264108, 304000, 304010
(04362) 264120

Shobhit University
NH- 58, Modipuram
Meerut, Uttar Pradesh
(0121) 2575091, 2575092, 2950279, 2950323
9810649492, 9319491700
(0121) 2575724

VIT University
Vellore, Tamil Nadu
(0416) 2243091, 2243093, 42016555, 65480555
(0416) 2243092, 2240411, 26222555