Middlemarch is usually cited as Eliot's masterpiece but I've always preferred Daniel Deronda: it might not be quite so successful but I think that's because Eliot's ambition is higher.
Set in England and Europe, this tells the intertwined stories of Gwendolen Harleth and Daniel himself. Eliot's portrait of Gwedolen's marriage, in particular, is a brave piece of writing for its time. Exposing the material basis for marriage that is glossed over in Austen, for example, it follows this to its logical conclusion.
Concerned with ideas of race and gender, this is a very modern novel in lots of way, wrapped up in Victorian style and format.