Which one is better for pursuing biotech among IIT, Kharagpur and IIT, Madras? Which one has better career opportunities?

IIT Kharagpur has better opportunities.

Both of them are excellent institutes, however,IIT Madras has better rankings. Since you are getting the same branch in both, you can decide by location as in which one will be closer to your home. Also you can check their website and have a look at placements for each.