From a purely technical standpoint Federer's is obviously (slightly) better. With Nadal's historic surface sweep, it's close enough to be an argument, but nothing more. Any notion that it's clearly Nadal's is pure fanboyism.
It is certainly close comparing Federer 2007 and Nadal 2010.
Federer won 3 and 1 RU. Nadal won 3 and 1Qtr Final.
Federer has the better overall record, but Nadal won on 3 surfaces.
Very marginally Nadal.
Federer won and Nadal RU.
Federer 2. Nadal 3.
Advantage Nadal, but Federer won on clay and hard court. Nadal's were all on clay.
Federer won 8. Nadal won 7.
Overall very similar years and little to split them despite the posts of the biased Federer and Nadal posters on this website claiming one to have had a clearly superior year. Except for Laver in 1968 no other player in the open era has achieved more in a year than either Federer in 2004, 2006 and 2007 and Nadal in 2010. Connors in 1974 and Wilander in 1988 being the only other player other than the 3 players already mentioned to win 3GS in a year in the open era.
My feeling is that by retirement Federer and Nadal will be considered by the objective poster to be the greatest two players of the open era. Obviously conditional on Nadal winning a lot more before he retires which at 24 which is not unrealistic.
Option 3 is the only sensible answer.