@Mukigachar - Your question is focused on a MS, but I thought it could be worthwhile to share what I learned about PhD admissions, which are based on many of the same factors.
There have been many posts on this subject and I think the consensus for technical (STEM) PhD admissions is that your undergraduate school may be a factor, but it is minor compared to grades, research experience, letters of recommendation, and GRE’s. I thought that it might be useful to collect just a little data, based on my son’s current plans. He will soon have completed his junior year at Texas A&M and is on track to graduate next spring with honors and a degree in aerospace engineering. He has decided to go right away into graduate school to pursue a PhD, focusing on electric/plasma space propulsion. Based on our research, the top three colleges that have laboratories that train PhDs in this area are Michigan, Princeton, and Georgia Tech. (There are other great PhD aerospace engineering schools, but many do not focus on this field. So, additional words of advice are to figure out what you are really interested in, not just what school you want to go to.)
I decided to look on the laboratory websites and see where graduate students have come from in recent years. I added up current post-docs, 2016 PhDs, PhD candidates, and PhD pre-candidates (admitted but have not yet passed qualifying exams).
The Michigan Lab is the Plasmadynamics and Electric Propulsion Laboratory. http://pepl.engin.umich.edu/. 12 people met my criteria. They came from Arizona State, Yale, Michigan State, Georgia Tech (2), Missouri University of Science and Technology, Southern Cal, McGill, Maryland, Columbia, and Michigan (2).
The Princeton Lab is the Electric Propulsion and Plasma Dynamics Laboratory. http://alfven.princeton.edu/. Five people qualified. They came from Caltech (2), Penn State, Indiana, and University of Alabama, Huntsville.
At Georgia Tech, the lab is the High-Power Electric Propulsion Laboratory. http://mwalker.gatech.edu/hpepl/ Seven people qualified. They came from M.I.T, Georgia Tech (3), Texas, Cal Berkeley, and one not specified.
So my conclusion for this very small sample is that the top university PhD programs in this field draw from some of the top undergraduate engineering institutions in the country, but smart students from other colleges were also admitted. (This field is more applied physics than it is traditional engineering. Several students graduated from college with physics degrees.)
One other observation, two of these labs also provide data on where they are placing PhDs. This seems like very important information to have before selecting a PhD program.
Michigan’s PEPL PhD placements from 2010-2016: Post-doc @ PEPL (2), Aerospace Engineer at Lockheed Martin - Skunk Works, Research Scientist at NASA Jet Propulsion Laboratory, United States Marine Corps, R&D Engineer at Space Systems/Loral, LLC, Palo Alto, CA, Technical Staff, MIT Lincoln Laboratory, Lexington, MA, Product Development Engineer, Federal-Mogul Corporation, Naval Research Laboratory, Research Engineer in electric propulsion, NASA Glenn Research Center, Air Force Research Laboratory (Wright Patterson AFB), Research Engineer in electric propulsion, NASA Glenn Research Center, Research Engineer in the High-Power Electric Propulsion Laboratory at Georgia Tech, Atlanta, GA, and Research Scientist in electric propulsion, Air Force Research Laboratory (Edwards AFB).
For Georgia Tech’s HPEPL they did not specify the degree earned (Masters or PhD) or the year of completion. Nevertheless, it’s an impressive list: Propulsion Vibroacoustics Engineer, NASA Marshall Space Flight Center, Postdoc at Naval Research Laboratory, Postdoc at Los Alamos National Laboratory, Manufacturing Manager, Lam Research, Independant Consultant, CERN, NSF Fellow, Massachusetts Institute of Technology, Captain, United States Air Force, Thermal Engineer, Zinn Technologies, Electric Propulsion Development Engineer, SpaceX, Research Engineer II, Georgia Tech Research Institute, Senior Consultant, Booz Allen Hamilton, Assistant Professor, University of Brasilia, Technical Staff, The Aerospace Corporation, Naval Research Laboratory, Professor of Aerospace Engineering, University of Alabama at Hunstville, Propulsion Engineer, NASA Glenn Research Center, Nuclear Fusion Engineer.
(I would note that Professor Mitchell Walker, the Georgia Tech HPEPL Director, earned his PhD in 2005 from Michigan after many years with their PEPL.)
There is one other factor that comes to mind that I have not seen discussed on this forum. What kind of connections do the faculty have that will be writing your letters of recommendations? My son has been fortunate here. Texas A&M is just starting its own plasma research programs. Dr. Ken Hara is a 2015 Michigan PhD and PEPL alum and also did a post-doc with Princeton’s Plasma Dynamics Modeling Laboratory. He has just started A&M’s Plasma Dynamics Modeling Laboratory. My son is just finishing up Dr. Hara’s special topics class in Electric Propulsion. Texas A&M also just hired Chris Limbach, a Princeton PhD, specializing in Plasma numerical simulations. My son has signed up next fall for Dr. Limbach’s special topics class in Computational Fluid Dynamics. He expects to be doing a joint research project next fall with both Dr. Hara and Dr. Limbach. So if all goes well, my son will have both classroom and research experience in his field and should be able to get solid letters of recommendation. This is still a relatively niche research area and everyone pretty well knows everyone else.