I couldn't find a list of best colleges for MS in Instrumentation Engineering.

Here are a few colleges that offer instrumentation courses.

Excelsior College
Salt Lake Community College
San Jacinto Community College
Boise State University
Sinclair Community College
Modesto Junior College
Moraine Valley Community College
University of Alaska Anchorage
Joliet Junior College
Idaho State University
Ozarks Technical Community College
Public Merced College
Amarillo College
Fox Valley Technical College
Public Lakeland Community College
San Juan College
University of Alaska
Moraine Park Technical College
Cincinnati State Technical and Community College

If you know more, please post here.