I would say Shock Troopers is the best shooter, but most people consider it a run & gun rather than a shooter.
Blazing Star and Pulstar are generally considered the best shooters on the Neo Geo, but they are also outrageously difficult and not all that accessible for a beginner to try to 1cc. Last Resort also has some difficult parts. So I would say that other games like Aero Fighters 2, 3 are also contenders for the best on the Neo, as they are reasonable prospects for the average gamer to 1cc (i.e., you don't have to be an insane player like BBH to finish them on one credit).
No one said Alpha Mission? Can´t understand why, it´s really an amazing shmup...
Alpha Mission 2 has a lot of atmosphere. I like the music and graphics.