A decent way to get about 5000 tune points and 7000 nyan points is the last mission of the Plus campaign "Wanna be an Angel"
Command skill is Kakizaki's special and Auto skill Crusher that does double damage to large ships.
Just take out the first few waves of the drones and VF-11Bs. When the Ghost shows up use Kakizaki's special to nuke it.
Then on the second part get up close to the SDF-1 and use the special, which will wipe it out in one shot.
Don't know if anyone's already doing it to farm for some points.