Where can I find the last model ship?

Some stores sell them late in the game. Also there is a small alcove to the left of the elevator that is easy to miss on the bottom deck of your ship (where James is). Just past the weapon bench. I found one there kinda late though not sure if it's the one you're looking for. Otherwise they're just spread out around the Normandy. Also there's some in the platform under the three Engineer's on the engineering deck.

One in the corner of the life support room as well tends to be missed. Also at some point you can get the space hampster back. It runs around in the bottom of engineering. You just need to catch it. Fast little bugger.

I'm having the same issue. I've played thru twice and still haven't found that top left model of the case on the wall. Did the perfect ending too.

The model on the left in the cabinet to the front of you is the destiny assention and the model on the left in the other cabinet is the shadow brokers ship. the destiny assention i think i found on a mission not sure, the shadow broker ship that came with the shadow broker mission dlc on ME 2 think it just carried over.

Actually, I found the Destiny Ascension in the room Thane had.

The top left bracket for the right display case is the Normady SR1. I found it in the very beginning of the game down where James and Cortez stay. it's on the left side past where you danced with James.

The ship your after is deffo the shadow broker ship and its found in the walk way under the engine room (jacks room from me 2). You must have completed the shadow broker mission pack in me2 and picked up the model from the shadow brokers ship. If you did this in 2 it appeared on the table next to the model cabinet as it was to big to fit in.

The entire Shuttle Bay,

below the Engineering Deck (aka Jacks former hidey hole),

try Thane's old room (aka the empty room in the Crew Quarters Deck next to the lounge - not Kaiden/Ash's room)