Which one is better: PGDIE at NITIE or MTech in nanoscience at IISc?

It all actually depends on your interest. As both of these options are completely different and two different areas of interest. You must choose what you find interesting. There would not be any conflict between these two institutes over the placement stats as both of them will give good placements to their students. Here are the recent placement highlights of the institutes.

If you are interested in tough work that is more challenging or research and development-oriented, you should choose IISc. As in the world of Nanoscience, IISc is the country’s most renowned institution. And if you are more inclined towards managerial work, then it would be better to go to NITIE.