The new command creates will have a possibility to drop reputation items, now i do not know if that includes rep for the vendors on fleet or not so it will be worth keeping an eye on.
You earn Command Crates every time you rank up a Command Rank. These are RNG loot crates containing various items, one of which is potentially a gear upgrade for you.
A random un-modded outfit piece or weapon
A random gear piece fully modded with a chance of having a set bonus
A random chance to get a crew skill schematic
A chance of getting Jawa Scraps, Rank 5 or 6 Companion gifts, or a reputation item
The above was taken from Dulfy's site.
http://dulfy.net/2016/11/29/swtor-galactic-command-guide/