AIIMS Patna is the better option when compared to AIIMS Jodhpur. Check the following points for brief info:
AIIMS Patna is the best option, however, some may reject it considering the environment in Bihar. But Patna is the education hub without any doubt where you can enjoy learning among the great minds of the country.
AIIMS Jodhpur is a better option. It has a well-functioning hospital. There are around 400 beds. It has already started MD and MS courses. The number of seats at AIIMS Jodhpur is the most among all the new AIIMS.
It offers admission in five-year MCh Pediatric Surgery courses. Other than AIIMS Bhubaneswar, it is first among all the new AIIMS, to start super-specialty courses. As far as MBBS is concerned, faculties, academic environment, research exposure at AIIMS Jodhpur are great.
Between Jodhpur and Patna, the former will offer a better city life. PG coaching facilities at both cities are quite similar. Considering all these factors, I will suggest that you choose AIIMS Jodhpur, given the option.