Putting aside the number of victories & other merits, and concentrating on sheer driving skill, some names from 1950s-70s come to mind. I don't know other eras that well. I would consider the best judges to be F1 drivers themselves, and top motor writers like Denis Jenkinson.

1. Alberto Ascari
2. Juan Manuel Fangio
3. Stirling Moss
There seems to have been quite a contemporary agreement on the virtuosity of these three.

4. Jim Clark
5. Dan Gurney. Jim Clark mentioned that Gurney is his most talented rival.
6. Jackie Stewart, from 1968 onwards: the '68 Nürburgring victory sounds pretty formidable.
7. Emerson Fittipaldi. Everyone seems to agree that he was a great driver, and would have won much more without Copersucar.

Of the more recent decades, I am convinced that at least Gilles Villeneuve and Michael Schumacher would have been greats in any era.