B.Tech ECE pass-out with CGPA 9.4, 3 years of exp. as SWE. Aiming for Universities in USA for MS in CS having better internships/job opportunities after graduation. What are my best options?

Your CGPA is absolutely terrific, and with that amount of work experience, you can get into any college and get a well-paying internship. Before I recommend you any universities, let's take a look at the eligibility criteria:

UG/degree Bachelor's in Computer Science or a related technological subject with a least 3.0/4 GPA.
GRE - The GRE is your ticket to a top university in the United States. For the top programmes accessible, you will have a score between 300 and 335.
IELTS/TOEFL - To demonstrate your ability in the English language, you must have an IELTS band score of 6.5 or a TOEFL score of 90.
Relevant internships/job experience/projects - Depending on your work's relevance, quality, and results, these might surely provide an edge to your profile.
Now here is a list of universities that you can target:

Massachusetts Institute of Technology
Stanford University
Carnegie Mellon University
University of California
Harvard University
Princeton University
University of Washington 
Columbia University 
Cornell University
Just ask me if you want to know more about any of the following universities.