Trivia: When he was filming The Perfect Storm, Mark Walhberg lived in a small room above the Crow's Nest. That's where his character, Bobby Shatford lived in real life.
Trivia: The film is accurate in its depiction of how the Perfect Storm actually formed (a combination of two weather fronts and one dying hurricane) except for the depiction of Hurricane Grace; in the film, it's stated to be a Category 5, while in reality, it was only a Category 2.
Answer: Not a ship captain, but will take a shot. If a massive wave is close to cresting, as I seem to recall in this scene, the boat would have to climb a near vertical wall of water and would likely be flipped back and upside down by the advancing wave. Perhaps he was planning to gun the engine to penetrate the wall of the wave, and bob to the surface after it passed. Reversing the engine would just let the thousands of tons of water in the breaking wave smash down on the boat, crushing it.