I just finished with the stealth cruiser and beat the last boss with this set up (on normal):
Weapons:
Mini beam
Dual Lasers
Burst Laser Mark II
(Total of 4 energy

Drones:
Defense Drone MK I
Defense Drone MK II
(6 energy, but in hindsight, I could have done with less, perhaps just the MK I in combination with the cloak might have been enough, but then I might have to take a few hits, as opposed to take no hits at all.)
Cloak III
No teleporter
It was surprisingly easy, actually. The boss couldn't hurt me much at all, I think I lost about 3 or 4 hull damage in all three phases. Basicly I tried to save my cloak for the moment he launches his rocket volley, and just get through his shield with my lasers and minibeam three rooms (starting at the shields, in order to get them down). But the two defense drones worked really well. It was the longest boss fight I've ever had, in the first phase especially, I missed too many lasers many times in a row and couldnt get through shields and use my minibeam, but the stealth cruiser is made to survive!

My score was in the 4900's, but I had to spend a lot of scrap on repairs in early game.