I've added collections to the LibraryThing catalog of the Mather Family Library, so it's possible to more easily see the breakdown of where the books are now (those that we know of, anyway). Not surprisingly the AAS leads the way with 1,482 known titles; the MHS follows well behind with 94, and then there are a smattering of others (Harvard with 60, Yale with 27, the Huntington with 13, &c. &c.).
I also added collections for the books Cotton Mather purchased as duplicates from the Harvard College library in 1682 (some of which are now back there), and for those books we know came out of the Thomas Shepard libraries.
Of course these numbers will change as we're able to confirm more locations, which I hope to be able to do. There are 95 titles I have as "Present Location Unknown," so if you can help me decrease that number, I'll be eternally grateful (I'm sure some of these are now in institutional collections).