SSV Normandy SR-2: Find this on the Hyperion, in Alec Ryder's quarters above the bed
Alliance Dreadnaught: Find the Black Market dealer in the Kadara slums (he's in a shipping container that you'll have to jump to get to, in the southwest corner of the slums). The model is on a crate right next to him.
Destiny Ascension Model: In the lower levels of new Tuchanka- just outside the little alcove with the shaman who kicks off Rising Tensions, the model is on a large orange-trimmed crate against the wall.
Initiative Shuttle: Right next to the holoprojector, after you've founded the colony on Kadara.
Initiative Fighter: In Spender's Apartment, when you search it during Drack's questline. This is the only chance to obtain it, and it is technically theft. So, you know.
Turian Frigate: On a table two rooms north of Priya in the Voeld colony.
Athabasca Class Freighter: Along the west wall of the Initiative Embassy on Aya, once it's founded. Far left end of the counter, looks like another piece of kitchenware.
Ark Hyperion: In a small out-building in Prodromos, south of the Tempest, on the east edge of town, but not quite so far east as the building Yale hangs out in. Find it on an incubator-like device by the wall-window.
Nexus, NOMAD, Archon Ship, Citadel: All these become available at the General store aboard the Nexus over the course of the game.
Kett Fighter: In Outcast Headquarters in Kadara port, on a crate just across from the holding cell.
Kett Shuttle: Buy this from Thrasia in the Varren Scalp windfarm on Kadara, just a short drive west of Kadara port.
Angaran Shuttle: On the leftmost desk in the flight control room at the Angaran Docks.
Remnant Fighter: Purchasable from the general goods merchant in the Aya market.
Remnant Derelict: This will show up next to Alec Ryder's computer after completing the main story quest.
Tempest: Automatically added to your inventory after completing the Movie Night questline.