I beat the boss last night on easy with the Engi ship. But I got MASSIVELY lucky. After 2/3 jumps into the game, I got an augment that boosted any scrap I got by 15% (can't remember the exact %). I also seemed to get exactly what I needed, when I needed it: 2 fuel left, found a guy trading fuel for missiles; trouble destroying ships, find 2 weapons in as many jumps; not perfect upgrades before final boss, kill someone and get over 150 scrap for it.
On attacking the boss I had a full crew (2 Engi, 2 Human, 1 Rockman, 1 Manta, 1 Zoltan), starting ion weapon, 3 shot blaster (Kestrel's starting weapon), a single shot blaster (with enough power for all 3), 2 attack drones Mk1 and 1 defence drone Mk1 (enough power for 2). No cloak/teleport.
---Possible spoilers for those who haven't faced the boss yet---
Against the weapons only, I just made sure I paused after each volley he shot, moved people around and aimed for his shields with everything. I probably should have switched my 1-shot blaster to taking his weapons out.
Against drones I took his shields first, then kept shooting my Ion at them to keep them down. Used other two weapons on the drone control - constant fire on this meant that he was taking crew damage too, so couldn't keep everyone in there at the same time to repair it.
Against the teleport, I got lucky. 1st group teleported into the air-lock area, so I opened that which helped when they reached my crew. Then the 2nd two went against my Manta/Rockman. 3rd two were difficult (mainly because of other damage) and almost destroyed my ship, but I survived with 3 hp left. Multiple hull breaches, fires in most rooms, everyone on low health (except the pilot who was oddly un-harmed).
---End possible spoilers---
My tip would be to make extensive use of pausing the game to take stock of what's going on and move crew around to where they're most needed. Also, have a mix of quick/long reload weapons. I didn't need missiles/bombs but it would no doubt have been much easier with a fire-bomb.
Now to try it on normal!
