First of all, the cheapest ship module to reach max level on is the Patrotlic Administration Center, which is the very first one. The whole thing requires 570 common, 450 rare and 40 super samples.
This guide will mainly be about gathering super samples, as I have already made a solution on the best way to get common and rare samples here:
Super samples are usually all found in the same place on the map in stacks of 3-5 depending on the difficulty. They only spawn from Suicide Mission difficulty (Number 7) onwards. They usually surround a tall, rounded, stone structure that somewhat resembles the shape of a mushroom.
The best way to find the super samples is to find the radar dish sub-objective, which reveals everything on the map including where samples are located and will be marked on the map by a jewel looking symbol. Usually, one of these jewel markings will be the location of the super samples, so make sure to visit every one.