The choice generally depends on the certain individual and what he prefers. Both of these institutes started in the same year. They are both new NITs so they come with their fair share of pros and cons.

• One of my friends did his Master’s from NIT Meghalaya. According to him, it still has a lot to work on and improve, be it their infrastructure, research grants, etc. 
• The permanent campus is under construction.
• The Electrical Engineering department has better-equipped labs than the other departments.
• If you are willing to pursue a Master’s program then it is recommended you opt for any other college rather than the two mentioned.

NIT Uttarakhand and NIT Meghalaya are both tier 3 institutions, so the outcome of graduating from these will definitely differ. Though NIT Uttarakhand has been known to improve their placements every year. But they have a lot to develop to reach the status of tier 1 or 2 colleges.