Theirs a simple way to look at this. Survivability.
The most effective vessel in the game is the one with the highest survivability and combat effectiveness. At its simplest, the ship that can bring weapons to bear fastest will fire first, and will cause damage first. The most manouverable ships is the winner every time, purely because the more sluggish vessel cannot acquire the target, and thus cannot fire. (asuuming comparable pilot skill, you said best ship, not best pilot
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)
The Eagle has the best turn rate of the VHF's, and as a result, can run rings around the other two. It can remove itself from trouble faster, and can acquire the target faster, meaning it does damage while the enemy is still trying to bring his weapons to bear. The armour increase means little, as the weapons are insanely powerful at this level, and shields are all the same anyway... so it comes down to handling characteristics.
Eagle. Simple.