I would use a command line interface with python, but I know you would prefer C# or java. If you want to make a graphical interface use java, but I do not know much about C#, only C++. if they are alike with the libraries, then use C# for a command line interface like on linux.
first answer on stack overflow, hope I did OK, good luck with your project!
solved To comunicate with arduino should I use C# or Java? [closed]