Boult has a slightly better average, but Wagner has more wickets per match (over 4), better strike rate and is less dependent on the overhead conditions and new ball. Also Wagner would be a strong contender for a world test XI, while Boult wouldn't be.
Thought I'd have a look at the stats over the last couple years.
On the face of it it's not even close:
Wagner: 72 wickets at 24.41; SR 48.9
Boult: 80 wickets at 30.63; SR 59.2
Southee: 68 wickets at 33.45; SR 63.3
Henry: 22 wickets at 48.5; SR 88.4
That's not surprising, but what I found interesting is that despite everybody clamouring for Southee's axing and praising Boult's genius, the difference between the two of them is pretty moderate. Looking at the stats in a bit more detail though, the reasons do become apparent. Firstly, Southee has been by far the most inconsistent of the three bowlers. Looking at their records against individual countries, Wagner and Boult's standard deviation from their overall average is about 7 runs. Boult only averages 40+ against 1 country (Australia, whom he played against during a period when he was recovering from a stress fracture). Wagner doesn't average 40+ against anybody. Southee's standard deviation from his overall average is 17 runs, and he averages 40+ against Australia (9 wickets at 62.77), England (8 wickets at 49) and South Africa (8 wickets at 44.37).
That's the other area where Southee's record falls down a bit. His record against the big 4 opponents (Aus, SA, Ind and Eng) is poor. He's taken just 37% of his wickets against these teams, despite playing 55% of his matches against them, and his average against them rises from 33 to 52.48. By comparison, Wagner's taken 46% of his wickets against the big 4, at an excellent average of 27.21, while Boult has taken a monumental 64% of his wickets against the big 4, at a good average of 33.63. That's the one thing statistically that makes it hard for me to say that Wagner is our best - Boult's sheer wicket taking consistency against top opposition sides, even when hampered by injury. Boult also genuinely outbowled Wagner in India, which should put paid to the idea that Boult is condition reliant for his wickets.