Eagle in Icicle is pretty good as well. It has incredibly high health and defensive stats. In terms of bossing, it doesn't fall too far behind Great White Shark (Lv45 in thundoria), though you can feel the difference in attack. It's definitely the best boat for Sea PK where there's multiple seavoys involved.
GWS on the other hand is probably much better for farming items such as LB set, Quality Caviars or just about anything sea mob-related, as it deals a lot more damage than Eagle, and this is quite noticeable on mobs, also the better boat for mini sea bosses. As opposed to Eagle, this one rocks in Sea PK where the enemy side doesn't have Sea Voys. It's worth noticing that Eagle is generally more level-dependent as opposed to GWS.
So each of these boats is awesome in their own sense, though my personal preference was and always will be Eagle. Many might argue for and against each ship, but it all comes down to whether you prefer a high-defense ship or a high-attack ship, along with the pros and cons which come along with it.
You also mentioned Goddess, the lv40 ship in Shaitan. It's an all-purpose Boat which is weaker than both of these, but it's a pretty good ship nonetheless. I mainly plant those across Isles in Magical Ocean or have one around for near-Shaitan needs or one docked in Treasure Gulf, Skeletar isle and etc (Mystery Harbor). It's a good and "quick", cheap ship, but it's definitely not worth leveling up as it doesn't scale as good as GWS or Eagle do.