The most obvious parallel is that both stories deal with a shipwreck, but I imagine you are looking for something a bit deeper than that.
Junger tells a story of what happened to the ship the Andrea Gale. He is working off of pieces of information only, and thus speculates in order to fill in the gaps. He imagines what would have happened to the boat, how it could have been sunk, what the men would have been doing (based on their personality, which he develops well through conversations with loved ones), and how the men would have died. It is a convincing story, but it is speculation.
In Life of Pi, the Japanese officials are desperately trying to discover what happened to Pi and to the ship, and they - like Junger - are working off of spotty information. The have to piece together the truth out of Pi's allegorical "animal" story. Unlike Junger, however, they do have a survivor, and he does eventually tell them the true story. That story, and the animal story, have many similarities. This is the same in The Perfect Storm, in which Junger's "story" and the small fragments of details and debris discovered have many similarities.
Finally, there is a parallel in theme. Life of Pi discusses how identity is shaped and controlled by the niche in which one's life has been forced. An animal is controlled by his genetics, and by his place in the food chain. A human is the same, and change the human's niche, you change the behavior. Pi is a vegetarian, but not when stranded on the boat, where he becomes a voracious carnivore. In The Perfect Storm, Junger spends the first half of the book explaining the behavior of the fishermen based solely on their town and their job. Their niche, in other words.