The monster convinced Victor to create a female companion for him and blamed his destructive demeanor on loneliness. He promised Victor that he would avoid humans if Victor consented. However, Victor changed his mind after reviewing the likely impacts of his promise and destroyed the creature before she was complete.

To conceal his work, Victor placed the destroyed creature in a basket and added stones to ensure the basket and its contents sank to the bottom of the sea. Under the cover of darkness, he put out to sea and dumped the basket.

Victor remained at sea and fell asleep. When he woke up, he did not know his exact location. He was convinced that he would die at sea, and this got him thinking about Elizabeth, his father, Clerval, and the monster. Victor was worried that the monster would go after them because he failed to fulfill his promise.

“Fiend,” I exclaimed, “your task is already fulfilled!” I thought of Elizabeth, of my father, and of Clerval; all left behind, on whom the monster might satisfy his sanguinary and merciless passions.

Concerning Shelley's Frankenstein, Victor puts the remains of the female into a basket and drops it into the sea from his boat, during the night under the cover of clouds. 

As far as who Victor thinks about when he is on the sea, your question is a bit vague, since he's on the sea more than once.  I'll assume your asking about when he is on the sea for an extended time, narrating his tale to Walton.  In short, he thinks about everyone involved, since he's narrating the story.  But, specifically, other than when he's narrating, he is probably consumed with getting revenge upon the monster.  Thus, I suggest he's thinking about the monster, and destroying him.