I can't make " New-Nios II Application and BSP from template".

Yes, also working on Windows 7 64bit :

If you don't see a NiosII menu item on Eclipse,

or File => Run -> Nios II C/C++ Application and BSP from Template

Un-install all Altera packages, delete all Altera files, reboot, re-install NiosII with Eclipse.

Then one should have the NiosII menu items, including "Nios II C/C++ Application and BSP from Template".

If get a .bsp but no application :

Run Eclipse in XP sp2 compatibility mode. I have administrator privileges. Say yes if get a run confirm window.

Then run "Nios II C/C++ Application and BSP from Template".

Should now run through OK.

Build Application (right click).

Use NiosII => Quartus II Programmer menu item to connect to hardware, upload .sof file.

Run application as NioII Hardware, making sure you refresh the USB connection if needed (on extreme right of window if pops up).

Should now all run.

Best of luck.