how to check the NIOSII code footprint size

If you need to fit code into internal memory, it is probably best to avoid as much of libc as possible. The hello_world_small template does some of that - but, IIRC, it still has sizable chunks of libc code.

If you can remove all references to malloc() and free() things will be much safer! but that may require you write your own startup code (about 4 instructions!) and may stop you using any of the jtag uart functions or most of the Altera hardware drivers.