In my openion LISER is better option as you get 2 yrs time for Msc project and only 1year time in NISER.As you need some time to accomadate in the lab and undrstand the project completly.And if you take seriously then you can easily able to publish some paper in 2 years time.You can also eligible for direct interview in BARC if your CGPA is 7.5 or more.