Population is not a data set we have a good handle on, but we do know a lot about the size of territories. I'm going to assume that by "Ancient Greece" you mean the Classical period to the end of the Hellenistic period. The following list is drawn from Hansen and Nielsen Inventory of Poleis Appendix 9. All of these had territories (we guess) >= 500 km2. There are ~2x as many as here in the next category down, 200-500 km2. In bold here are the especially large.

Sicily: Akragas, Gela(?), Himera, Selinous, Syrakousai

Epeiros (northwestern Greece): Kassopa, Korkyra

Boiotia (central): Tanagra, Thebes, Thespiai(?)

the Korinthia/Megarid: Korinth

Achaia (western Peloponnesus): Elis (probably not very populous)

Arkadia: Kleitor, Megalopolis (after Spartan break-up), Tegea(?)

Messenia: Messene(?)

Lakedaimon: Sparta

the Argolid: Argos, Epidauros(?), Hermion(?), Troizen

Attika: Athens

Euboia: Chalkis, Eretria, Histiaia/Oreos(?), Karystos(?)

the Chalkidike: Olynthos

Thrace: Abdera, Ainos(?), Maroneia, Byzantium, Perinthos, Tyrodiza

Pontos (west coast): Apollonia, Istros, Kallatis, Mesambria, Odessos, Olbia, Tyras

Skythia/Pontos: Chersonesos, Herakleia, Sinope

Asia Minor and coasts: Kalchedon, Kios, Kyzikos, Lampsakos, Parion

the Troad: Abydos(?), Kebren

Ionia: Chios, Ephesos, Erythrai, Miletos, Samos

Karia: Halikarnassos (with dependencies), Knidos(?)

Rhodes: Lindos, Rhodos

Pamphylia: Perge, Side(?)

Cyprus: Amathous, Idalion, Karpasia, Keryneia, Kourion, Lapethos, Marion, Paphos, Salamis, Soloi

Libya/Tripolitania: Barke(?), Kyrene