The sea is not directly referenced in the third stanza. There are two ways to look at the other images in this stanza. The "stately ships" suggests ships that they are majestic, moving slowly, and in grand style. This could be an image of a funeral procession and therefore the speaker sees this as an homage to his lost friend. But given the speaker's general tone of grief and frustration, he may just be noticing the ships but not caring about their superficial stately maneuvers. Or, he might be implying that the stately ships (and those on them) are so far away that they are beyond the speaker's cares: perhaps mocking the upper classes who sail on such ships who do not care about the problems of common people.
The ships go to their haven (which sounds like heaven) and this is "under the hill" which again suggests a funeral procession to a grave and afterlife. This is one way to look at it, but it could also be that the ships are going to a safe place (a haven, guarded by a hill). This contrasts with the speaker's position: being in a vulnerable place. The ships are safe and comfortable; the speaker is vulnerable and grieving amidst an indifferent sea. (This is the recurrent image of the sea: that the sea is indifferent to the speaker's cares.)
He longs for the "vanish'd hand" of his loved one who has died. He longs to hear this person's voice - the "sound of a voice that is still." This word "still" means that he longs for a voice that is motionless (which would make time motionless) If time had stopped prior to this person's death, he/she would still be alive. And if this person was still alive, he/she would "still" be there to talk and listen.