Could this be the 1980 movie "Cyborg 009: Legend of the Super Galaxy"? (Wikipedia refers to it as "Cyborg 009: Legend of the Super Vortex")
Despite the popularity of the "Cyborg 009" manga, which spawned three different anime series in the years from 1968 to 2002 (the second of which was broadcast dubbed in many countries, and was a great success in Europe), this particular movie seems to be quite obscure, so much so that it's difficult to find a summary longer than a handful of lines.
Anyway, the whole movie can be easily found on YouTube, and from a quick glance it could be what you are looking for.
- The spaceship looks like a large sled with wings.
- The commanding bridge was on top of it.
Here is the ship inside some kind of dry dock: I would say if fits your description
- The spaceship started on the water, maybe in the ocean.
Dr. Gilmore and the 9 cyborgs find the ship under the sea, and they make contact with the peaceful alien inside it (at about 00:12:00).
Later on (at about 00:36:00) the ship emerges from the sea and launch into space.
- The crew could drive into the battle stations with ball-like structures to defend.
On the bridge, the crew member (the 9 cyborg and the alien they are helping) sit on round pods (for example at 00:40:50).
Later on (00:54:30) they are attacked by enemy ships, and some of the cyborgs use the moving pods to reach and man gun turrets.