When you say strongest ships, do you mean offense, defense, or durability (hit points)?  The Iconians have a number of unique techs that give them the highest HP ships and high repair rates, but their weapon techs are weak.  Generally, if an Iconian ship isn't killed outright, it will be back with the self-regeneration techs.

The Drengin get a bonus in research weapons techs, and if they choose Evil with Xeno Ethics, get access to some powerful, but expensive weapons techs.  However, any race selecting evil can do that.

I haven't played the Arceans who are the other official warrior race, so I don't know the strengths of their tree.

As for building a custom race, you might want to play with both the Areceans and the Drengin, and then see which tree best suits your play style.  But if you want to plunge in right away, just go with the Drengin tree and select Military Production, Weapons, and Hit Point bonuses for your customization points.  However, I would suggest a full +30% in Economy: the early economy is very fragile, and neglecting means it will be a long time before you can build a large fleet and crush all the other races.

Quality also equals economy. If you can't afford to build the ships when you need them, of what use are the techs?

And you can have all the money in the world, but if you don't have the techs to defeat your enemy - of what use is it?

You have to be able to balance everything.

Ok, I just realized that I have actually to choose the techtree of one race. I thought before I could combine tech trees. Therefore some of the confussion ight have come from.

I like the Altarians, they gain techs fast.  However, their military bonuses are usually in defense, not offense.  While the Iconians soak the damage with their unusually tough ships, the Altarians avoid getting hit.  Still, if your race is higher tech than the enemy, it doesn't matter if you have special weapons or not.  Oh, when playing with the Altarian tech tree, who have to choose good: nearly all their race-specific perks are good-only.

Perhaps you should read TA 101 (https://forums.stardock.com/310907). It sums up the differences between the races in Twilight of the Arnor.  That should help with the decision process.

With the organic hull research branch, Iconian ships are all but invincible. Interestingly, in light of the fact that the AI rarely uses hull modules, the Iconian AI has actively pursued this path and built some pretty amazing ships. It's one of the main compensations for the Iconians' horrible early economy.