one thing to note is that the same ship can have different raritys. higher rarities WILL be better then the same version of a lower rarity. if you want to know the rarity of your ship look for diamonds on the left of your ship icon and name. the more diamonds the higher the rarity and thus the better the ship (3 diamonds is the max rarity, no diamonds is the lowest and thus the worst).
if you are wondering where to find ships of a higher rarity they are scattered across the galaxy shops so you may have trouble finding them, but on the chickeninvaders forum there is a topic where they try to keep track of where the legendary parts currently are so that may help you find them.
as for the specific ships, each family and induvidual ship has its own strengths and weaknesses so lets go over them:

H&C comes with the advantage of keys dropping more often for you. the disadvantage of this ship type is that they have the least satelite slots, the least hardpoints for cosmetics and among the lowest firepower, making them the worst overall
THE HATCHLING is the most extreme case of this, with the lowest firepower, hardpoints and satelite slots but giving the largest key drop bonus. it is however the fastest of the H&C family.
THE COCKEREL is the strongest of the H&C family with more firepower, hardpoints and satelite slots, but it provides the smallest key bonus and its the lowest of the H&C family, and given that you are only using this family for the key bonus, you might say that the cockerel is the largest dwarf.
PULLET is effectively a hybrid between the hatchling and the cockerel, sitting inbetween both in both the key bonus, speed and strength, but since you are only using H&C for the keybonus again hatchling is best from this family

Muller (M40) family is meant to be the "jack of all trades" kind of ships. they are the second slowest ship class and have the lowest satelite slots after H&C, but they have the second highest max firepower. if you want a well rounded ship, a muller fits the bill.
as you will notice, the cheapest model is again the weakest in term of firepower due to its 2 satelite slots, but also again the fastest of the muller series (this is a pattern for all families, the cheapest is weakest but fastest, the most expensive one is strongest but slowest).
overall id say deliverer is best from the muller family, because of its odd satelite dock count allowing you to place a satelite in front of the ship (usefull for destroying projectiles).

BX has the most destructive power of any ship with double damage pylons for double the projectiles and the second highest satelite dock count. they are however much slower then any other ship, causing their movements to sometimes lag behind. since this ship is all about firepower MJOLNIR is without a shred of doubt the best ship of this family, having the highest firepower and the second highest sattelite slots possible with an odd number of slots (5)

VF series is pretty unique. they produce the fastest ships with the most satelite docks of any family. they are also the only family that breaks the tradition of the more expensive ships having more firepower, with RAVEN having the weakest firepower at 8 and STARLING the highest at 10. this is because the VF ships have resistances against certain enviroments like massive. the more expensive the ship the more enviroments you can deal with without worry, but this advantage becomes moot if you dont have an enviroment to resist. so the best ship here depends on what you are looking for. if its raw speed its STARLING, if its to deal with tricky enviroments and most satelite docks its RAVEN. id say jackdaw is kinda pointless unless you truly want that odd satelite count as it doesnt resist as much enviroments as RAVEN and isnt as fast as STARLING.

as you can see, not 1 ship is clearly superior to another unless they are the same ship with different rarities. they all have their strength and weaknesses, and while some are definantly worse then others, wich ship you should pick is largely decided by what it is you need the ship for, wether it is key collecting, blasting chickens or surviving an enviroment.
hopefully this guide has been helpfull in helping you decide wich ship you should take the next time you visit the shop. happy hunting