I recall a similar attempt a few years ago, where two guys had set their minds on pedalling around the world. They had built a small boat driven by a propeller via a propshaft from a central crank case with pedals attached. Imagine a large canoe with a waterproof cover. They successfully managed a few legs of their trip, despite a few mechanical issues, but they didn't get along well, so they split up and one of them kept going by himself.
http://news.bbc.co.uk/1/hi/uk/7022644.stm
http://en.wikipedia.org/wiki/Expedition_360
Not exactly a sub, but at least similar in terms of propulsion...