The negation is "either neither of my cars was stolen, or both of my two cars were stolen". Apologies for "either neither", which might sound funny.
Of the two alternatives you provide, the correct one is "The number of my two cars which were stolen is not equal to one." It's not ideal, because now you're primarily talking about numbers, which the original statement doesn't mention. After all, the original statement isn't "the number of cars I had was two, and the number of cars stolen from me is one", although that's equivalent _in a language rich enough to talk about numbers_. However, the original can be (accurately enough) expressed in first order logic without any explicit mention of "one" or "two".