Notorious QED

I'm a physics/math double major with a minor in CS applying to CS masters programs for machine learning. My first letter is from my research advisor who I've been working with for 2+ years. The second is the department head who decides who decides who gets awards in the physics department; I literally hit every award and I also aced an upper level class with him, so I assume he thinks positively of me. I have two choices for my last letter of rec: A math professor. Basically took a class and did well. She's actually my research advisor's wife, and my advisor has told her about me. Probably doesn't help the letter though. A collaborator in my research group. She's a faculty member in the physics department of another university and I've been presenting my work to her ever since I started my project. Honestly, she's not crazy about me, but she said she is willing to write a letter. I feel that it would be kind of lukewarm because, like I said, she's not crazy about me. Because I'm applying for ML, I thought it might be beneficial to get a letter from the math department. But that's would not be a research letter. Then again, a letter from my collaborator would be a lukewarm research letter. My advisor is going to write a very good letter, so I also worry about the contrast between the two letters--one being really awesome and the other being lukewarm. All that being said, who is the better option? Edit: typos

I'm a junior (pure) mathematics and physics double major and I have decided to pursue a masters degree in computer science upon graduation. One of the professors at CMU exposed me to Python during high school, and he basically planted the seed. Taking a course in computational physics last year reinvigorated my love for the computer science and programming, so here I am now! My general question is: what can I do to best set myself up when I start applying to schools next year? Here's some background (just so you know what credentials I have as of right now): 3.91 GPA I've been doing research in particle physics for about a year. Trying very hard to publish before I graduate. I will be doing an undergraduate thesis in physics based on this research My advisor (full professor, had him for two of my courses) thinks very highly of me and will write me a solid letter of recommendation 2 academic awards for physics 2 research fellowships I will be able to complete a computer science minor (and then some) before I graduate. What should I be doing to make my application more attractive? Projects? More coursework? Will my physics research be seen as favorable, or should work a computer science internship instead? Would it be bad if I got my letters of recommendation from math/physics professors and not computer science professors? These questions immediately come to mind, but there are many, many more questions to consider. Any advice at all would be helpful!