Ok, your description of yourself sounds exactly like me....
Sorry, I just felt the need to say that....
I honestly think your boyfriend meant what he said. If he thought you didn't look good, he would have probably just said "oh, no, you are pretty" and wouldn't have said that your natural beauty is amazing.
About your eyebrows, if you really don't like them, try getting them professionally waxed.
About the dark puffy circles, cucumbers work, and also, if you don't have cucumbers, wet a facecloth and put it in the freezer for about 20-30 minute, then fold it and put it over your eyes for about 15 minutes. (But if it's too cold, wait! Don't let it freeze to your face please!) And, these circles could also be caused by eating too much meat or dairy products, and if that's not it, you may have done what I did and rubbed your eyes. If you do that so much you get puffy circles, there is no turning back.
Now, for your self esteem, everyday as soon as you wake up, look in the mirror and tell yourself 2 things you love about yourself. It doesn't just have to be about your appearance, it could be about your personality, too. An example would be "I love how I can make people laugh" and "I love my strong legs"
Just remember, you are beautiful :) Hope this helped