Valid question. If I could go back in time, I'd have started my masters after my first year and second deployment in my ops squadron, taken one class at a time and spent the left over time studying and being sharp at flying. I could have still easily had it complete at 03 + 6 months. Instead, I spent my entire first assignment (5 years) being really good at my job and deploying a bunch, only to cram the masters in while training on a new platform and deploying in a far more complex environment; and I finished 1 week after my board met. I did fine, got a DP, had the other boxes checked, etc. but it was more painful than it needed to be and I could have been just as good at flying and still gotten it done had I been better at time managment.
But the lesson I'd pass onto you would be: use your judgement to decide when you've estabilished a knowledge foundation in your platform. Once you're on solid ground and can spare about 5 hours a week, start your masters and take it slow. Be the guy who can always volunteer for a a TDY and is still awesome at your job, and take 3 years to do the masters if thats what you need. NEVER be the young guy asking for a day off the flying schedule to write a paper, you'll lose a respect you can never get back. But also use some strategy and don't be the guy who is cramming for his masters 6 months before his board meets like I did. There is a middle ground, you're a smart dude (or you wouldn't be doing this) and I'm sure you can find it. It won't hurt you to not have a masters as an LT, but if you can get it done while simultaneously being shit hot you'll impress people. Good on you for asking, and I hope this advice was helpful.