I have owned both the 5906 (and a 915) and the Sig 226 (and a Sig 225). The Sig shot more accurately for me and I loved the de-cocker and lack of a manual safety (small wonder that the 225 is my carry gun). However, the 5906 and the 915 before it were decently accurate and I like the way they fit my hand better; they just feel a little more comfortable. I was lucky enough to find a 5906 that was made without the magazine disconnect, though I never had any problems with it when I had the 915; I was always a little afraid, though, that, if I ever used the gun in a real shooting situation, and had to reload, I might end up breaking the disconnect by slamming the magazine home too hard from adrenaline.
I think the best one would be the one that fits your hand best and shoots best for you; in my case, it's a split decision - one's more accurate for me but the other feels better.
They are both first rate guns, though.