What he said does make sense. Your numbers are incomplete. You're saying "All firearm deaths" which include drive-by's, hunting accidents, etc. If you can't break down the numbers to ONLY those children who died from a gun that was stored in their own house and children who died in a pool in their own back yard, then you aren't making valid assessments of the multiple at all.
It's simple math.
That's exactly what he's saying though - that the Freakonomics article does NOT break the numbers down sufficiently, for either Drownings nor Gun Deaths. As such the 100x figure they came up with is bogus.
And yes, the Maths is simple. But gathering the right figures to plug into the Maths is hard.
Plus as I said, the drowning statistics above are a huge over-estimation as they don't give individual breakdowns of the context of the drowning (e.g. pools, boats, bathtub, etc).