Is It Better To Work Out In The Morning, Or To Do Stretches And Yoga?

Only you can determine which is better, so you need to experiment with yourself and see which works better for you. And the answer does not have to be either this or that either. The answer to your question may be a little of both, perhaps alternating days with one, then the other.
Keep a journal and try to observe yourself as honestly as possible. Try to get up at the same time every day so you can isolate the other factors and see which routine your body responds to.
Some people are morning people and some are night people. Many night owls would find it very hard indeed to wake up at five in the morning and run five miles. Morning folks thrive on this.
Running, working out, doing yoga are all good for you, so you can’t go wrong with any of them unless you overdo it. My suggestion to you is to do both every morning if you can. If you have one hour for your routine, I would break it down to ten minutes of light calisthenics, half an hour of running, and twenty minutes of yoga after your run,
The answer to your question is that you alone can monitor your body’s response to exercise and adjust your routine accordingly. For instance, if you try the above-mentioned program, and you feel exhausted the next morning, try rejuvenating by doing an hour of yoga only the following morning. If you are running one morning, and you find yourself like a horse which has been penned in too long wanting more, go ahead and run for fifty minutes that day. If your knees begin aching, you may want to switch from running to swimming.
Play it by ear. Keep a journal and be honest with yourself. Congratulations on your good attitude about wanting to get fit.