I agree - the cities are Paris and London.
The lives of the main characters are intimately associated with both cities. Lucie Manette is born in France, raised in London, returns to Paris to rescue her father who has been imprisoned there for eighteen years, is married and has a child in London, and finally is back in Paris at the time of the French Revolution. Charles Darnay, of the unscrupulous aristocratic line Evremonde of Paris, renounces his family, takes up residence in London, returns to Paris during the Revolution, and is almost hanged there by the peasantry.
The setting of the narrative moves back and forth between the two cities throughout the novel.