Since you already have a 9mm I'd suggest going for the .40 - with ammo availability the way it is these days it's nice to have more than one option. I love my Sig Pro .40 and I really wouldn't be too comfortable solely with a 9mm for home defense, however I struck out on finding .40 ammo in my last two attempts but there was still 9mm and .357 Sig in stock, which left me kicking myself for not having the .357 Sig replacement barrel for my gun and also convinced me that it's time own a 9mm again. Being stuck low on ammo for weeks at a time sucks.
That said, certainly shoot both guns if you have the chance, always makes the choice easier.