First of all, welcome to the ranch!
If you already know that your program will run on Windows, in my humble opinion your choice should be C#, assuming that you are equally proficient in both languages.Why C# ? It's undeniable that .net languages offer better integration with Windows OS. Given the nature of your project - a CAM - I suppose you will need soon or later to work with devices like plotters, printers, and drawing pads, and on my experience using .NET for such tasks it's just easier than with
Java