nvcc is not on your PATH environment variable when you are in MATLAB. When you start MATLAB by way of icon, it does not go through login and so your shell configuration files are not executed to do any customization of environment variables for you.
You should use setenv() within MATLAB to add the directory that nvcc is in to PATH, or else you should alter your system PATH environment variable to include the proper directory, or else you should put a symbolic link from one of the directories that is on the system default PATH to the actual location of nvcc
Example:
p = getenv('PATH');
setenv('PATH', [p ':/usr/local/bin'])
