yea the boss is all about knowing which weapons to take out, you should kill all but one of the crew in their compartments to prevent them from repairing in the future. the rest of the crew you can kill, leaving 1-2 alive after the first encounter makes it a breeze. always take out the triple missile launcher first... thing will ruin you!
Engi ship totally rules of course. First boss kill I think was with that ship.