Hondarake is really good! Very cheap, and the books are great quality for 2nd hand. You can also buy a set of books in bulk for alot cheaper. e.g. I think they had RG Veda for $30 (vol 1-10).
If you get lost; its in the middle of the street that its situated on, kind of opposite Wagamama. If you're coming from Darling harbour, its just after the new city zoo.
Morning Glory isn't really an anime store though

There's also an anime/figurine shop opposite Market City (central) in the building opposite; I'm not sure what its called but it has a restaurant on top. But it's a small arcade leading onto george street, with other clothes shops inside as well.
Theres also HobbyCo (which isn't strictly anime but they have a few things there ^^;) in Town Hall.
I hope you have a good time!
