Is it okay to have 2 strong and 1 good recommendation letters for an MS in Computer Science in the US?
You need to send in the letters that give the best impression of you, based on what is important to the admissions committee. 

For example if you are applying to a thesis based program at a top school and your proposed research area is theoretical and your three strong letters are from well respected academics, I would use those.

If on the other hand you are applying for a non-thesis based more applied program or are applying for an assistantship; your work ethic will be of interest to the committee.  I would use the internship supervisor letter.