The 2004 model. Most track fastest lap times were made in 2004, and of them, most are held by Ferrari.
Lap best times:
Melbourne - M. Schumacher - 1'24''215 (2004, Ferrari)
Sepang - J. Montoya - 1'34''223 (2004, Williams)
Sahkir - M. Schumacher - 1'30''252 (2004, Ferrari)
Barcelona - F. Massa - 1'22''680 (2007, Ferrari)
Istanbul - J-P. Montoya - 1'24''770 (2005, McLaren)
Monaco - M. Schumacher - 1'14''439 (2004, Ferrari)
Montreal - R. Barrichello - 1'13''622 (2004, Ferrari)
Magny - Cours - M. Schumacher - 1'15''377(2004, Ferrari)
Silverstone - M. Schumacher - 1'18''739 (2004, Ferrari)
Hockenheim - K. Raikkonen - 1'13''780 (2004, McLaren)
Hungaroring - M. Schumacher - 1'19''071 (2004, Ferrari)
Sorry, I haven't got time to complete the list at present. But as you can see, from these 11 races, 7 were won by the Ferrari 2004 car, 2 were won by other cars in 2004, and two were won in other years (Ferrari, 2007; McLaren 2005). While this isn't strictly good statistics, it does show the 2004 year was definitely the fastest year, and the Ferrari 2004 was the fastest car.
And the best car? It depends a lot on how you measure this, but if one looks at most championship points (assuming no change in scoring system): According to Wikipedia MS scored a record 148 points / 13 wins out of 18 races. If you add to that the win by Barricello in 2004, that makes at least 14 wins out of 18 races.