The main ship upgrades are: Ship armour, energy shield, shield regenerator, beam charger, beam generator and missile magazine. There are 7 levels for each of these upgrades (the 7th level was added to the game in patch 1.6).
The first odd numbered upgrade levels (level 1, 3 and 5) are all available for purchase with credits from a vendor on the fleet station. The even numbered upgrades (2, 4 and 6) tend to be a bit more valuable as they often increase more than one thing. For example an odd numbered ship armour upgrade will only provide an increase to the ship's armour. For example a grade 1 Grade 1 Ship Armor upgrade will provide a +1 bonus to ship armour. A Grade 3 Ship Armor upgrade will provide a +3 bonus to shp armour. A Grade 2 Ship Armor upgrade, however will not only provide a +2 ship armour upgrade but will also provide a +2 bonus to ship damage. The even numbered upgrades are generally made by players with the cybertech crafting profession (though many of the schematics are not common). Even numbered upgrades are also included as rewards for completing certain space missions.
The level 7 upgrades introduced in patch 1.6 are available in a variety of ways. They may be purchased with cartel coins. Other ways to get them include purchasing them for fleet & daily commendations or crafting (cybertech). Each of the upgrades has a note on how the grade 7 version of that upgrade is obtained.