Yes, there is difference between .gitconfig and .git/config.
.git/config will have the configuration details of your repository. But .gitconfig will have your user details and the configuration you set for git like user.name, user.email, default editor, color setting, etc.
In Windows, you will find the .gitconfig file in C:\Users\user_name.
.git/config file can be located under /.git/ (.git/config gets created once you run git init command or you clone an initialized repository).