Personal preference aside, I would probably have Sparta as the militant counterpart to Athens (which I view as scientific, rather than cultural btw.). The dichotomy between the Delean and Peloponnessian league just works very well.
Hell, I'd rather have Mycenae or Crete.
While Sparta/Lakedemonia is the archetype of the Militant Civ historically: they produced notable warriors and Olympia runners, but no philosophers, writers, or artists of any kind that we know of - even surviving art depicting Spartan warriors is from places like Athens or Corinth.
But Athens as Scientific is more of a stretch. The principle Greek philosophers from Athens were pure philosophers - Plato, Socrates and their immediate followers - who didn't add much to scientific thought although they were giants of philosophy. Aristotle founded his school in Athens, the Lyceum, but he came from Asia Minor and didn't actually work in Athens that long. The other giants of early Scientific thought from Greece: Heraclitus, Euclid, Pythagoreas, Hippocrates, etc al - none from Athens.
Athens' main claim to 'scientific' prowess would be the Lyceum and Akademe schools founded there, but the Akademe was almost entirely philosophy rather than 'practical' science, and they were founded in Athens because Athens was the largest Greek city in Greece - and even then both were founded outside the city walls to avoid confrontations with more conventional citizens and laws: Athens was always more friendly to philosophical questions and questioners that didn't seriously challenge the Status Quo as understood than those who questioned your entire view of the World physically or ethicially - see Socrates for what happened when you ran afoul of Athenian public sentiment.
Sorry, going on too long on too little. Bottom line, I think Athens with a Athens-specific Acropolis Cultural UD would give a Cultural basis for the Civ, with Athenian Leaders like Solon, Cleisthenes, Themistocles or Pericles giving a choice between Commerce, Diplomacy, Military/Naval or Government bonuses as desired.
The general Greek UD could be the Agora - a Commercial District that also gives Culture and Loyalty bonuses to reflect its place as the lively center of every Greek city - except Sparta, the exception to almost everything Greek!
And the Peloponnessian and Delian Leagues make good additions to Sparta/Athens because the two cities dominated their respective 'Leagues", but if we are going to nod towards the Greek Leagues the inclusions should be the Aetlian or Arcadian Leagues that were actually leagues of equals and so something different from the classical City State rather than "Warsaw Pacts" of their day dominated by a single Polis.
And finally, I would love to have Mycenea as a Civ: you could even justify "semi-mythical" Leaders like Agememnon or Nestor or Odysseas and either a Military or Trade emphasis.
Crete, on the other hand, is problematical: they are marginally better than, say, Harappa or Olmecs because we can put together an actual City List since the Greeks re-used so many of the original names, but we really don't have a named Leader: 'Minos' was probably, from context, a Title rather than an individual name. Doesn't make it impossible, but between the problems and the fact that Phoenicia really covers the same Naval/Trade niche in the early game, it becomes a "nice to have" rather than a Requirement.