What does this mean: "Credit card balance within $2000 of card limit"?

Yes, within $2000 of a $3000 limit would be equivalent to a balance of over $1000.

There is a slight ambiguity on the edge case where a balance of exactly $1000 might, or might not, trigger the alert as within could potentially be interpreted to be "this amount or less" or "strictly less than this amount", although for your use case, it probably isn't terribly important.