Jaffa is the old port-city near which Tel Aviv was built. I've always assumed the orange was named for it.

btw, the native pronunciation of the city name is yafa (hebrew doesn't have a "j" sound; e.g., "jerusalam" = yarushalayim). I mention this because yafa is the hebrew word for "beautiful". I presume that's the source of the city name, but have no further information.