One factor is the weapon type and another factor would be the weight of the weapon.
Pistols have low action point costs because they are small and light weight which makes them easy and quick to aim. Rifles are heavier than pistols so by default, it cost more action points to use them in VATS. Heavy weapons like mini-guns and fatmen consumes the most. They are big, heavy and unwieldy which take more time (and action points) to aim.
The weight of the weapon would be another factor even for the same type of weapon. If you have one 10mm pistol that weighs 5 and another that weighs 6.5, the heavier 10mm pistol would cost more action points to fire.
I am going to assume the weapon's fire rate also plays a factor. The higher the fire rate is the less time in between shots which means less action points. So for example, a .44 pistol has a fire rate of 6 while the 10mm pistol has a fire rate of 46. Due to the faster rate of fire, each shot of the 10mm pistol should cost less than each shot with a .44 pistol. But this is pure speculation...