Let the boil work for you

For a long time, I stirred food coloring into lollipop syrup after it had boiled and cooled off a bit. It worked pretty well, but usually there would be a few little tiny feathery bits of food coloring that didn't fully incorporate into the syrup, leaving behind little streaks that looked a little wrong.

I don't even remember where I read this suggestion anymore, but I started adding in the food coloring to still-boiling syrup after it entered the soft crack stage (>275 degrees F) and letting the boiling action distribute the color. Now, the color in the finished lollipops is very evenly dispersed and looks great in my opinion. Here's a photo of blue food coloring a few seconds after it's been added to boiling syrup:

Photo by Kevin Keeker