Depends what you mean by 'best', but in general the Drover is the most cost effective. It is ideally loaded with fighters as opposed to bombers, as the ship system will increase the wing size when active. Most combinations will work, though double Talon is a bit light and the ship has enough OP for a full missile load and the medium sized fighters. Double Sparks is of course the power load as Sparks are incredibly overpowered. Bombers are still ok as the system helps get wing sizes back to max very quickly (can double launch strikes if you activate after the first wave has fired, as returning craft count as 'dead' to the rebuild system).
Heron is also good and is more survivable thanks to its higher speed, and is ideally loaded with strike bombers thanks to its +50% damage system (note: needs to be activated before the bomber launches its payload, as the buff is applied to the fighter and then to the torpedo at launch time). Broadsword + 2 strike ships works quite nicely, though if you are already swarming with fighters the distraction is less needed, in which case longbow + 2 HE bombers is good as well.
Astral is the glass cannon of the bunch. It is vastly less survivable than the others because of its very low speed, but it has a very powerful system for bombers with Recall Device: it lowers casualties, doubles the strike frequency, AND vastly helps fighter replenishment rate as its not ticking down during the bombers fly back period. Best loaded with strike bombers - 2 longbows and then HE of choice works well, and while not ideal broadswords can be used in a pinch. Also, large missiles are great for standoff fire support.