I started writing about the pros and cons of the various storage methods, but then I realised this problem has a very simple argument that demonstrates the preferable usage scenarios of antimatters and black holes:
The black hole cannon would be used in space combat, correct? Because using it in atmospheric combat seems even more unnecessary than using megaton bombs or fusion instigators.
So it would probably work somewhat like this: compress M mass units of matter into a black hole, attach it to a container and then fling it at the enemy and have the container stop working at the appropriate time.
Or to simplify it further, attach the compressor automanipulator on a standard coilgun shell (weighing M mass units), fire it and activate the automanipulator when in range of the enemy ship.
The operation of the antimatter equivalent could be simplified as the following: Load a standard coilgun shell at the ship's normal cannon. Attach an antimatter converter automanipulator on it. Fire the slug and then convert it to antimatter as soon as it exits the barrel of the coilgun (or if it's cheaper, have the coilgun be a vacuum and convert it before firing it, since it will presumably retain the same physical properties).
So in the first case, assuming the black hole converts its entire mass to energy, we have M mass units equivalent amount of energy released somewhere near or on the enemy ship.
In the second case, the antimatter shell would release 2*M mass unit equivalent amount of energy somewhere on the ship (plus a probably insignificant (compared to the energy released by the annihilation) amount of kinetic energy), assuming it hits and all of it is annihilated.
So a black hole cannon would have less energy released and would be slightly more complicated to use, since depending on how you build it it can depend on two automanipulators, but you are certain that all of its energy will be released, even if it doesn't hit, allowing you to use it as a sort of flak cannon. Still, not all of the energy would reach the intended target without a direct hit, since it would radiate towards all locations equally, with the intensity dropping with relation to the inverse square law.
An antimatter cannon seems slightly simpler to implement, since it only needs one automanipulator and it can produce twice the amount of energy with the same mass, but it needs to hit the target for it to work and it is likely that not all of the antimatter will react with matter, bringing the amount of energy released somewhere below but still close to 2M mass unit equivalent amount of energy. You could increase the chances of it hitting a target by detonating the shell mid-flight, essentially turning it into buckshot, which would make it less powerful but more likely to cause severe damage assuming one of the fragments hits a ship.
Of course, in both conditions, not all energy created would be transferred to the targets since much would escape as radiation.
Plus, the lingering antimatter could keep travelling and ruin someone's day in the near or far future, while the black hole is more "environmentally friendly".
That is, assuming the act of converting a shell into antimatter and compressing a shell into a black hole require a roughly equally priced automanipulator.
Price could become a factor once you start weighing in that you could create antimatter conventionally, without the use of automanipulators, so then it would become a question of whether or not it is preferable (read cheaper and easier) to create automanipulators or antimatter and whether or not the risk of storing antimatter is greater than the risk of storing automanipulators.
Don't forget, automanips can be as dangerous as antimatter. Who's to say that a stray shot hitting your automanipulator storage won't cause an overload that would cause your entire ship or even nearby ships to collapse into a temporary black hole or have your entire fleet ripped apart by gravity distortions?
So, those are my thoughts on the two weapons. It all depends on what you want. Black holes seem to be "safer" but less destructive, while antimatter seems more destructive but also a bit more reliant on good targeting and luck and overall slightly more dangerous. Both are stupidly dangerous and should be used with caution, if at all.