The US Pacific Fleet Submarine Force was arguably the single most efficient and effective organization in any Allied military in WW2 when considering the task assigned and how thoroughly it was accomplished.

Starting with about 45 large fleet boats (equivalent of the Type IX U-Boats). The US would eventually build 250 more through the war. So much smaller numbers than the +900 U-Boats between the VII's and IX's. And early war USN torpedoes were utterly trash with a whole host of problems that led to abysmal reliability.

But by August 1945 they had accounted for over 60% of the Japanese Merchant Marine. In 1941 Japan had about 6.5mil tons of shipping with another 4mil captured or built. By 1945 though 8mil tons had been sunk, about 60% of which or 5milwas by Sub, along with another 400k tons of warships. The hulls sunk being 1300 merchant ships and 200 warships(including several of their priceless carriers and battleships).

So 5.5mil tons and 1500 ships. While nowhere near the 20mil tons 6k ships the U-Boats had. However when considering the # of USN boats involved, the distances involved in the Pacific, the USN out performed expectations.

Now it should be admitted that IJN ASW practices were outright terrible to start the war and only sort of got better. To the level of just up and not setting depth charges to the proper depth. But still 52 Boats were lost on patrol, so between 20-30% of the total force, though higher when you consider not every boat made a patrol or served in the PTO. Meaning just over 3000 sailors if you figure 60 man complements.

So in the end the Submarine Force sank more than double the tonnage of Japanese ships that Carriers did, and arguably were absolutely key to the isolation and starvation of the home islands of resources. While also providing key missions such as reconnaissance and picket duty to rescue downed aviators, including the first President Bush!

Some good reading on the Silent Service against Japan:

http://www.anesi.com/ussbs01.htm#dotjmf: Strategic Bombing Survey(breakdown if shipping losses to causes)

Conquering Tide by Ian W. Toll: Excellent 2nd volume of his general history of the war.

Silent Victory: The U.S. Submarine War against Japan by Clay Blair one of the seminal works of USN Submarine history.