The story that you heard was a sub legend, documented in Clay Blair's Silent Victory. After what was thought at the time to be a record-setting patrol by Burt Klakring in USS Guardfish, the USN held a press conference, rare for the sub service, to give newspaper reporters some morale building stuff to write about for the folks back home. The reporters were shown a chart, and on the chart was a notation for "race track". A reporter asked about it, and Klakring, having some fun with the press, said that the crew placed bets on the ponies while watching the races. While it's true that Guardfish operated very close to the coast of Honshu, it was just a story, but it made for a great one, and newspapers all over America ran it.
As for harbor raids, there's some sub legend in that too. There were numerous cases of US subs making attacks on Japanese shipping at anchor. Examples of US attacks are Mush at Wewak, Street at Cheju-Do, and the various attacks on Matsuwa in the Kuriles.
But, the places chosen for attacks weren't harbors in the sense that people in the US and Europe think of a harbor as, like New York harbor or San Francisco Bay. Rather, these were anchorages that were open to the sea, where the trick was to avoid uncharted shallows and enemy defenses and deal with in-shore currents to come close enough to achieve a firing position on ships anchored next to shore, then get away alive....but not, like Prien at Scapa Flow, sailing miles up a narrow channel to hit a ship in a harbor.
SH4 gives one the impression that US subs snuck up miles of estuary deep into Japanese harbors to pick off ships at the dock, like in Tokyo Bay or the Inland Sea, and nothing like that ever happened. But, it makes for a great story.
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