To the best of my knowledge, there has never been a hoax in baseball quite like the one that is going on with Manti Te’o, but there have been a few “good” hoaxes:
Tim Johnson was the manager of the Blue Jays in 1998, guiding them to a surprising 3rd place finish that left them only four games out of the Wild Card. Throughout the year, he motivated his players with tales of his time in Vietnam. Only thing is, he’d never been to Vietnam. He’d been a reserve during the war and the most he ever did was train troops at Camp Pendleton. He was let go before the 1999 season and has never managed in the big leagues since.
Sidd Finch was a more good-natured hoax, a pitcher who was reported in the April 1, 1985 issue of Sports Illustrated to be able to throw a fastball up to 168 MPH. It was never meant to be taken seriously, an April Fools joke by George Plimpton. Still, some people apparently fell for it, despite the fact that I’m reasonably sure that a 168 MPH fastball is physically impossible for a human being to throw.
As part of his defense against his doping scandal this season, Melky Cabrera‘s handlers allegedly created a fake website that they claimed was for a supplement that Cabrera took that unknowingly contained banned substances.
There have also been phantom ballplayers, players who were reported to have played in the big leagues but who didn’t because the games weren’t official or, in some cases, were inventions of wisecracking telegraph operators. Wikipedia (which admittedly, shouldn’t be taken as a definitive source by any means) has an article on it.