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NEIGRIHMS Shillong is the better choice. In fact, it is considered among the top five institutes of excellence. It is a well-resourced premium central Govt. institute. While SNMC Agra is an old state medical college with limited resources. 

However, you should keep in mind that, NEIGRIHMS is located in a remote corner of the country. Whereas, SNMC is located in central India. At NEIGRIHMS, you will get better quality education. But at SNMC, you will get more time to prepare for postgraduate and better working options. 

If you are not from northeast, you can choose SNMC for UG and prepare for better options in PG.