I had the same issue last winter in my 66. All my windows would fog up & I had a little condensation forming in the trunk also.
When I took my back seat out I found 2 puddles of water under it. Used the garden hose & found my rear window was leaking at the bottom on both sides, running along the metal behind the back side trim pieces and pooling under the seat. Had the window resealed at a glass repair shop & haven't had any problems since.

 

I'd go with the heater core.The phrase, "it can't be the heater core cause I just repladced it", sealed the deal for me. Something isn't installed correctly. Look at it again.