Successfully complete the game, then enter the following codes in Honeycomb Lock mini-game to unlock the corresponding crate. The positions are described with "1" being in the top left and the rest of the numbers moving clockwise:

1 2 3
8....4
7 6 5

Unlimited ammo rail gun crate: 7, 10, 2, 10, 6
Unlimited ammo sub, machine gun crate: 2, 9, 1
Unlimited ammo suitcase gun: 4, 1, 6, 2