If you include V'Ger's energy cloud, which measures in at 2 Astronomical Units, or the diameter of Earth's orbit, so 186,000,000 miles, that seems to dwarf the asteroid Yonada.
And that's only if you go by "The Director's Edition"! V'ger was supposed to be 82 (!) AU's in diameter, so it's clearly the biggest thing anyone's ever encountered. I guess unless you count the space that Voyager traveled through to reach the Alpha Quadrant in "Endgame" as a vessel. I don't.