Scylla can be tough if you're not expecting it, but if you treat it like a series of tough ship battles it's not so bad. Keep an eye on your ship health, drop anchor & heal up if you need to.
Hydra's a long tedious fight, but it seemed hardest for me at first and then got easier as it went. Keeping track of details (which heads you need to focus on and when) helps a lot.
For Witchdoctors, and considering what level you are when you run into them, the worst one is probably Bishop in the Beachhead main battery. (Witchdoctor enemies in general are a lot more formidible for us in the new worlds than they were through Mooshu.)
Hello Highlander Fox! I believe that, atleast for me, that the Hydra was the toughest for me. I found this boss to be the toughest because of all of its glitches. I thought that the Scylla boss wasn't hard, at all. I have some pretty neat ships, though.