Whether you farm ships from the fleet arena, galactic war store, or (preferably) both, you absolutely should focus on ships. I put a fair amount of effort into them as soon as I unlocked them, and within a few months I was regularly taking first place in my fleet arena. Six months later, I still do.
Also, remember that each fleet arena contains much fewer people than each regular arena, so it's quite a bit easier to score near the top in fleet arena. Quite honestly, fleet arena is the easiest place to score lots of crystals on a regular basis, especially for people in newer shards.
