As you have asked about the list of top universities in USA for Master of Science (MS) course, I am giving you some information about it, check below for the details

Massachusetts Institute of Technology (MIT)
Stanford University
Carnegie Mellon University
Harvard University
University of California, Berkeley (UCB)
Princeton University
University of California, Los Angeles (UCLA)
University of Washington
University of Texas at Austin
California Institute of Technology (Caltech) California Institute of Technology (Caltech)
Columbia University
University of Illinois at Urbana-Champaign
Cornell University
New York University (NYU)
Yale University Yale University
Georgia Institute of Technology
University of Pennsylvania
University of California, San Diego (UCSD)
University of Chicago University of Chicago
Brown University
Duke University
Pennsylvania State University
Purdue University
University of California, Irvine University of California, Irvine
University of Maryland, College Park
University of Massachusetts Amherst
University of Michigan
University of Southern California
University of Wisconsin-Madison
Boston University