I will say, top 3 for me. The Shuttle, my heart, the Squint, my soul and soon to be the blood that pumps in my veins, the Decimator. ( I love me my large ships, or my super fast ships )
Poll What's the best ship
Oh wait I forgot, the Corellian Corvette is the best ship. Duh! 
Tie Defender specially with a HLC!
My brother from another mother.
Sun Crusher
Echo (phantom)
I'm going to say two, one for each side.
X-Wing and TIE Defender.
For me, the best ship is Interceptor.
Moreover, the interceptor is the ship with the best potential for the entire game until the wave 5.
The title (royal guard tie) that allows equipping two modifications is a unique asset. A pity that the wave 3 and wave 4 have no modifications that might be used. I'm hoping to have great modifications cards in wave 5.
Take this opportunity to vent and complain about how the squad points are calculated. The real value of one ship should be for what it really you puts at the game table. While today you pay for possible upgrades that you can equip the ship.
If you want to fly with a tie bomber without any upgrade. What is the real price of it?
Or if you want to fly with an E-wing without any upgrade?
It would be nice if this points (upgrades not used) were removed from the ship's final value.
What use to be the ultimate ship if you can barely put one in your squad? We just try to put "one" sacrificing quality for quantity.
Firespray all the way
A-wing
Tie fighter
B Wing