If you want something more than top-exhibits, and more than Plaka museums, here is a list with updated information (Oct. 2018) about museums in Athens. There are four categories, first is the classical Athens, second is a thematic category, third more modern, and fourth museums related to contemporary art. We should also note here, than many museums from the first category host contemporary art exhibitions. So, a visit to the website or even a call is much useful.
Soon there will be more info about each museum.
Athens history- archaeological museums
Nicholas P. Goulandris Foundation – Museum of Cycladic Art, founded in 1986, hosting amazing collections of Cycladic and Cypriot art. Neofytou Doyka 4, Syntagma metro, +302107228321 http://www.cycladic.gr
National archaeological museum. Before the New Acropolis Museum, the most important museum. Patision 44 & Alexandras. Victoria metro station, +302108217717 www.namuseum.gr
Epigraphic Museum, housed in the south wing ground floor of the National Archaeological Museum. Tositsa 1, +302108217637
The New Acropolis Museum, Areopagitou 15, Acropolis metro station, +302109000900, www.theacropolismuseum.gr
Ancient Agora Museum, Stoa of Attalos, +302103210185
Kerameikos Museum, Ermou 148, +302103463552
National History Museum, Old Parliament, Stadiou 13, +302103237617, http://www.nhmuseum.gr/
Numismatic Museum, Panepistimiou 12, +302103643774 http://www.nummus.gr
Benaki museum (Main building) Koumpari 1 & Vas. Sofias (Syntagma metro) +302103671000, https://www.benaki.gr/index.php?lang=en
Goulandris Natural History Museum (GNHM) in Kifissia, north of Athens https://www.gnhm.gr/en/
Museum of the city of Athens, Paparrigopoulou 5-7, +302103246164 http://www.athenscitymuseum.gr/
Byzantine Museum, Vas. Sofias 22, Evaggelismos metro +302107211027 http://www.byzantinemuseum.gr/en/
War Museum, Rizari 2, +302107252974 http://warmuseum.gr/
Thematic museums
Jewish museum of Athens, Nikis 39, +302103225582 https://www.jewishmuseum.gr/
Irakleidon Museum, 16 Heracleidon Street (1st building) & Ap. Pavlou 37 (2nd building), Thesseio, +302103461981, http://herakleidon-art.gr/
Wine Museum, Petsa Avenue, Pallini,+30 210 6037933, http://www.mouseioinou.gr/moyseio
Ceramic Museum- Centre for the Study of Modern Pottery – G. Psaropoulos Foundation, 4-6, Melidoni str, Keramikos, +302103318491 www.potterymuseum.gr
Museum of History of the Greek traditional costume, Dimokritou 7, Kolonaki, +302103629513 www.lykeionellinidon.gr
Athens botanological garden, Iera Odos 403. http://www.diomedes-bg.uoa.gr/start.html
Athens University Museums
History of University of Athens, Plaka, Tholou 5, +302103689502, http://www.historymuseum.uoa.gr/
Criminology Museum, Medical School of Athens, Mikras Asias 75, Goudi, Athens, +302107462406 (please call first) http://www.criminology-museum.uoa.gr/
Zoological Museum of Athens, University Campus, Zografou, +302107274609, (please call first) http://old.biol.uoa.gr/zoolmuseum/
Pharmacology Museum, Medical School of Athens, Mikras Asias 75, Goudi, Athens, +302107462504 (please call first)
Museum of Paleontology and Geology, University Campus, Zografou, Athens, +302107274086 (please call first) http://paleo-museum.uoa.gr/paleontology/index.php?option=com_content&view=article&id=98&Itemid=30&lang=en
Industrial – technological museums
Railway Museum Siokou 4 Athens, +302105130300 http://sfs.gr/
Telecommunications Museum, Proteos 25, N. Kiffisia, +302106201899, https://www.otegroupmuseum.gr/portal
Industrial Gas Museum 100, Pireos str.Gazi, Athens, +302130109300,
http://www.technopolis-athens.com/web/guest/museum
Hellenic Motor Museum, Ioulianou 33-35, Athens, +302108816187 http://www.hellenicmotormuseum.gr/en/
Hellenic IT Museum (H.IT.M.) Petrou Spiropoulou 2 & Thessalonikis, Moschato, +302103007010 http://elmp.gr/
Athens Pinball Museum, Areopagitou & Makri 2, +302109245958 https://www.facebook.com/AthensPinballMuseum/
Modern – contemporary museums
Athinais Contemporary Art museum, Kastorias, 34-36 – Votanikos, +302103480000 http://www.athinais.com.gr/el/
Theocharakis Foundation 9, Vas. Sofias Avenue & 1, Merlin Str. Athens +302103611206 http://thf.gr/en/home/
National Museum of Contemporary Art, Kallirrois Avenue & Amvr. Frantzi Str, Athens, (Syggrou-Fix metro) +302111019000 http://www.emst.gr/en/
Vorres Museum, Parodos Diadochou Konstantinou 1, Paiania, Attica +302106642520 http://www.vorresmuseum.gr/