Monastiraki station has some left luggage lockers but they could be full & it might depend on the size of your case as to whether it will fit in them.
I've heard that the electric station at Pireaus also has storage facilities but you'll need to check that out.
I've also heard about a place that stores luggage close to the New Acropolis Museum.
the address is Veikou 3 Makrygianni 117-42
internet address is www. athensstudios.gr
You'll need to do some research to find out if these are suitable or maybe someone on here will be able to suggest which option is better.