Found a solution to my problem!
There is a variable called ModuleDirectory defined in ModuleRules which gives you the source directory of the project. I just used that to get my root project folder.
edit:
To provide an example I used this in my projects ModuleRules.
public string ProjectRoot
{
get
{
return System.IO.Path.GetFullPath(
System.IO.Path.Combine(ModuleDirectory, "../../")
);
}
}