Besides making another chowder, what can I do with leftover milk/fish stock/broth from a New England Fish Chowder?

Why not simply freeze it. Then pull it out and use as a base for another chowder, or a nice wild salmon soup, or use to make an exotic rice dish with clams or mussels or fish anything.
It is as endless as your imagination !

Ok, I don't know if this would work, but I wonder if you could use it as a base for some sort of seafood mousse or "flan"?

You could make a cioppino or a seafood pot pie sounds great.