Ok, I've looked over the stats on Eye Bots, especially as compared to Raid Starships and I really think Eye Bots aren't that far off. Their biggest weakness is they don't have speed to escape after popping like Raid Starships. But I don't think any of us want to see super-fast Eye Bots. (NOTE: I see speed 68 on Eye Bots and 296 on Raid Starships in a normal game)
The Eye Bots actually get a quite a few juicy targets from their Heavy multiplier, unlike the Raid Starship which gets Ultra-Heavy (basically Golems). Since you aren't really going to solo a golem with Raid Starships, that isn't really a big deal. But several Guard Posts, Guardians, and a ton of Spirecraft are Heavy armor which Eye Bots are great against. They are hilariously awesome against MLRS posts which they get x3.2 damage on and are immune to the return fire from.
So I think in the end, it might just be players haven't figured out how to use them properly. Their paper stats are quite good. However, I would consider upping their reload time and their damage (same dps) slightly. I'd suggest a reload time of 4 with a 33% damage/shot increase, or maybe reload of 5 with a 66% damage/shot increase. But that change should allow them to be more usable, either because they'll kill in the opening volley and be able to start fleeing 3 seconds earlier, or because they will get more damage out of each ship that dies in under 3 seconds.
If you don't like that, a touch more range (4k right now, maybe 5k which is just under Raid Starships) instead.