Not sure it was crabs, but pretty sure he had something or other.
http://www.doctorzebra.com/prez/g35.htm#x17Kennnedy had "occasional burning when urinating, which was the result of a non-specific urethritis dating from 1940 and a possible sexual encounter in college." This was left untreated and became a chronic condition by 1946. At some point the illness was described as "a mild, chronic, non-specific prostatitis." Sulfa drugs were able to suppress the symptoms. As late as May 1955 he still had "prostatitis marked by pain when urinating and ejaculating, as well as urinary tract infections". In January 1956 he underwent cystoscopy under anesthesia.
Comment: Was this a sexually transmitted disease? (1) The response to sulfa suggests it was infectious. (2) Kennedy had a large number of sexual contacts before he was even out of college, and (3) it seems unlikely he practiced safe sex. As one female acquaintance remarked, "He was not much for planning ahead".