"Stop this ship!"

He's talking about Pequod.

R + L = J

he's listening to Moby Dick on tape....

The Titanic. He wants them to stop cos he knows they're going to hit the iceberg. Really sad scene.

I suppose the ship he meant was the one from Moby Dick, which was playing over his phones.
He was saying stop the ship as he felt they are lost- lost in real life too.

Listen to what he is saying, he's calling Ahab a "Godless Son of a Bitch".

Ahab was dead set on finding and killing a great whale. So much so that he will risk his crew and ship to do it, it's either get the whale or die trying.

How much this alludes to the films plot is up to you.

The way I interpreted it was that Paddy was seeing Tommy as Ahab in that moment. Ahab was a character who lost a limb to the white whale and spent his life trying to chase it down again for revenge. In the process nearly all of Ahab's crew perished (including himself) and the ship was lost.

Tommy 'is' Ahab because he doesn't care about the fragile relationship they still have and would gladly watch it all sink rather than giving up his hate for Paddy who he sees as his personal white whale. "Stop this ship!" is what he wants to say to Ahab, or "stop this madness", and turn around and enjoy what life is left to live while they still can.

The Moby Dick thing is a metaphor for the madness of revenge. Tommy does actually stop the ship, though, because rather than being pleased that his father is now an emotional wreck, he decides to help him instead.