I wouldn't say it is early in the game. I have beaten it about hour ago. After playing for a more than a day, having saved for complete home base upgrade and the best gun (special bolt cannon) - 70000 for only those two items.
Not all of the above is needed, but some loot grinding seems to be necessary. The strategy that finally worked was
- get full stack of torpedoes (20, 6 remained after the fight). And as much air tanks as you can get - 10 wasn't enough for me, the fight was longer and I had to retreat for a refill
- it's probably good idea to put everyone who could help into combat station, you don't want to miss a shot at torpedo, leave some people on repair duty too
- wake it up, then quickly do 180 turn and retreat on overdrive and up. While retreating hold the forward button and look back to watch for torpedoes
- carefully approach again. Watch when it fires a torpedo, shoot it down when it's near enough and then dive for your own torpedo shot, then quickly rise back up to the safety. Repeat until it's dead, or at least all it's turrets are destroyed.
Main dodge method is up and down. All my other attempts (hide below it's belly and shoot at towers for example) ended badly because of the clunky controls.
BTW I chose the "fast" ship for my game. Slower ships may need to some other strategy.