I am making a flat design animated video for a non-profit and have to decide which program I want to use: Animate CC or After Effects CC? I am familiar with After Effects and have an idea of how I would animate the project in After Effects but as the program is called "Animate CC" I was wondering if this program would be better for me to work in than After Effects for animation. So the question is, what program would be better for animating a 2d scene?
This depends entirely on the style of the animation. AE creates video, Animate CC is designed for web based interactive content. The Character Animator is a great addition to the AE toolbox for some styles of animation. Without an example or a detailed description of exactly what you are trying to do that's about all the advice I can give you.
By "flat" do you mean you're going to be shooting stop-motion?