Oh, so many to choose from... I'll give a top-list.
1. The Raza, Dark Matter - Federal Gunship. If you haven't seen Dark Matter, you need to see Dark Matter. It is the closest thing to Elite: The Television Series I've seen.
2. The Nostromo, Alien - Type-9 Heavy. This ship launched a franchise that had grown to near-legend. Not quite the same though, as the Nostromo weighs in at:
Length: 334 meters (1096 ft.)
Width: 215 meters (705 ft.)
Height: 98 meters (322 ft.)
Mass: 63,000 metric tonnes
The Type-9:
Dimensions: 117.4L - 115.3W - 33.2H, Mass: 1000 tons
3. Moya, Farscape - Beluga. Not really, but it's about as close as it gets. At 209.1m in length, even the Beluga is utterly dwarfed by a Leviathan at 1.5km in length. Only the Farragut and Majestic class Capitol ships can compete for size at 2.04 and 1.9 km respectively. And as a living ship, the Leviathan continue to grow throughout their roughly 300 year lifespan.
4. SDF-1, Robotech - in basic form, either the Corvette or Farragut most closely resemble this, though the Farragut is closer in size. Unfortunately neither of these can transform, and perhaps fortunately neither produce protoculture.
5. SSV Normandy Mass Effect - FdL.