There are many fine choices but to me there is one that literally stands head and shoulders above the rest.
1) Das Boot is hands down, the best submarine film that I have ever seen and arguably the best naval movie ever made. The directing of Wolfgang Petersen and overall attention to realism are second to none and the acting and screenplay are excellent. It gives you a visceral sense of immersion in the boring and frightening world of undersea warfare that makes you part of the crew. Of course it is a film about a German U-boat, the enemy in our last great war, but that matters little since the film is about the trials, hardships, hopes and fears of men who fight on the seas and not about who they are fighting for or against or why, as exemplified by this quote by film character Lieutenant Werner:
They made us all train for this day. "To be fearless and proud and alone. To need no one, just sacrifice. All for the Fatherland." Oh God, all just empty words. It's not the way they said it was, is it? I just want someone to be with. The only thing I feel is afraid.
It is a film that leaves you thinking long after it is done.
2) Enemy Below is a splendid film, especially for its 1957 date, and the absolute best at showing the deadly game of chess between a Uboat and a destroyer (the naval equivalent of the wolf and the sheep dog) from both sides. Robert Michum and Curd Jurgens are both excellent as the opposing Captains.
3) Crimson Tide provides a riveting view into what at the time was a very real conundrum regarding the release of nuclear weapons under very trying circumstances. Gene Hackman as the commander of a nuclear missile submarine and Denzel Washington as his executive officer do a magnificent job portraying two different views on command, the world, war philosophy and current events and Tony Scott's is at the top of his game as director. The tension is so well developed you are half expecting the end of the world.
4) Master and Commander is the best film done yet about the Napoleonic Wars and one of the best naval films of any period. Again, attention to detail, excellent screen play and impressive acting performances by the stars and supporting cast bring this classic to life.
5) In Harm's Way is another classic and includes perhaps the best scenes about a WW II surface engagement done yet. Of course, Otto Preminger's epic covers a lot more than this, beginning with the attack on Pearl Harbor and ending a couple of years later with America's return to the South Pacific in force. John Wayne and Kirk Douglas are seldom better and Henry Fonda, Burgess Meredith, Dana Andrews, Carroll O'Conner, Slim Pickens, George Kennedy, Bruce Cabot, and Larry Hagman, are part of the excellent supporting cast. Loyal Griggs's handsome black-and-white photography is topped only by Saul Bass's impressive closing credits sequence, a rising cascade of crashing waves and rough surf that aptly suggests the cruel and unforgiving nature of sea combat.
My honorable mention list could be endless but would start with Captain Hornblower (surprisingly not mentioned yet) with the always classey Gregory Peck and some of my additional favorites would include in no particular order: The Bedford Incident; Tora, Tora, Tora; Run Silent, Run Deep; Midway; The Caine Mutiny; U-571; The Sea Wolf and Mister Roberts.