The answer depends on who you ask.
The WTB&TS says he was buried on Staten Island in an unmarked grave not far from the old Watchtower Farm on Staten Island.
People who were close to the situation claim that an empty casket was buried on Staten Island and that "the Judge" was buried on the grounds of Beth Sarim in san Diego, where he wanted to be buried and where his Watchtower buddies tried to get a permit for his burial. The city of San Diego denied the burial permit though, which gave the WTB&TS an opportunity to claim persecution. The word is that Nathan Knorr and one or two other Watchtower insiders buried him anyway under cover of night. Some say he was put into a hole near the edge of the property, while others say that he was buried under the floor of the garage. The garage would have certainly provided better concealment of the burial process, and the new concrete floor the garage received shortly after Rutherfor's death added further cover.
My money is with beth sarim, most likely under the garage. Maybe someday the property will be owoned by someone who is willing to have that garage floor torn up.