I think you're (SsZero) confused a bit about the nature of the reaction. The reason that a fusion reaction needs energy to get going is because actually fusing the nuclei of two atoms together requires an enormous force to push them together against the electromagnetic force, since they have to pushed very close for the strong force to become the dominant one. Once in this state, it is a lower energy state, so therefore overall energy is released. This energy can be used to force two more nuclei together and continue the reaction - effectively the very large energy barrier stops the reaction happening at room temperature.
With anti-matter / matter I don't think there is such a large energy barrier. Because an antimatter particle has the opposite electric charge, the two particles attract rather than having to be forced together.
However, one thing to note is that producing an anti-matter particle, currently, is achieved by giving a lot of energy (kinetic) to a particle and colliding it with others. The antimatter (and matter) particles are created out of the pure energy. Then the matter-antimatter collision produces this same amount of energy.
As a power source onboard a ship, antimatter doesn't make much sense, since as much energy is needed for the creation as is released in the collision. With fusion for example, the products of the reaction are more stable (lower energy) than the reactants, so overall energy is released. This isn't true of an antimatter reaction. However, due to the 100% mass-energy conversion, a lot of energy can be stored in a compact space. For instance, if 500g of antimatter was produced, according to E=mc2 then 9*10^16 joules of energy from the conversion of 1kg of mass was converted to energy.
In line with conversation of momentum, to give the ship momentum, you would need to throw stuff out of the back of the ship. This is what rocket engines do - expansion of gas gives a momentum to exhaust fumes in one direction and therefore the ship gains momentum in the opposite direction. If you could somehow use the energy to fire particles out of the ship at near light speed then the ship would gain momentum in the opposite direction.