I don't remember the specifics, but I know there are some real negatives about soy. Allergies, and I seem to remember something about learning disabilities.
Having said that, when my son was first born, and I did not have milk yet due to drugs I received during my c-section and the stress of having a baby in the NICU, he was given soy formula because he could not tolerate the dairy one. It was only for a little while, though (2 days) and he was getting breastmilk, too.
I would say that if you have been exclusively breastfeeding until now, that SOME soy would be okay. But how come you are giving him formula? If you've been nursing till now, i would try to keep it up until he's a year old and then you don't have to make this choice. If you are supplementing with some solids, he should be fine with just nursing a bit and having some solid foods.
I know this isn't much help because I did not use formula for long, but wanted to encourage you about nursing, since it's the best thing for him. :)