It has to be Peter Mattis, co-creator of the open-source image editor GIMP and a Google engineer. The clues are all right there in the Times article. A tipster helped lay them out for us.
"Harken Pretty" anagram: The apartment, once thought to be sold to movie stars Sarah Jessica Parker and Matthew Broderick, instead went to an LLC called "Harken Pretty," which is an anagram of the first names of the buyers, according to the Times. Mattis is married to Kathryn Kimball; the couple are pictured in the image at left, taken from Kimball's Facebook profile (here's Peter's profile). "Harken Pretty" is the most coherent anagram for the couple's first names.
Young family: The buyers have a "young family," just like the trio of Mattis, Kimball and baby in the picture above.
Used to live in SoHo: The Times' mystery buyers want to escape "the hustle and bustle and celebrity of SoHo, where the family now lives." Mattis and Kimball used to live at 56 Crosby Street, according to sales records, before putting the property up for sale earlier this year. (Mattis implied in the Times that some of his coworkers might be jealous of his new home; perhaps they could take some relief in the fact he had to cut the price of his old home twice, reducing the asking price by a total of $650,000.)
Money to burn: The new apartment costs about $3.5 million more than the current listing price of the old apartment. But judging by Mattis and Kimball's political donations, they have plenty surplus cash to spend. Campaign records show donations to three different candidates in the last presidential election by the couple: $2,300 to libertarian Republican Ron Paul; $4,600 to Demorat Hillary Clinton; and $4,600 to Democrat Barack Obama in Mattis' name and another $2,300 in his wife's name (see here and here).
We've emailed Mattis at Google, Facebook and two old Berkeley email addresses. We'll let you know if we hear back. UPDATE: Mattis called; he wasn't happy to see his family plastered on a website and went out of his way to say he wasn't telling us anything on the record. (The photos above were taken from the public front of Mattis and Kimball's Facebook profiles.)