Up the sanctuary steps and through the left door is la capilla used for morning services. On Monday, August 17, 2008, I found 8:15 a.m. benediction (closing adoration?) and 8:30 Mass. In between a litany was offered that called upon Mary with the various patronage titles that honor her in the countries of Latin America. The parish bulletin listed also a morning mass at St. Malachy's rectory. Capuchin Franciscans (long ago, German in heritage) staffed St. Michael's, and on Warwick Street a large building has the sign "Capuchin Friary." The Capuchin Province of St. Mary has headquarters in White Plains, New York.
Above is Salve Regina Catholic Academy, 237 Jerome St., Brooklyn NY 11207, telephone 718-277-6766. It is on the northeast corner of Jerome Street and Liberty Avenue. Click on any photo to enlarge it. Apparently, some school buses serve St. Michael's. On Atlantic Avenue, just north of the church, is bus route Q24, from Jamaica to Bushwick.
As for the church of St. Malachy, a final Mass was offered there in there in January, 2009. From the second link below, it would seem that the church was soon demolished.
Historic photos of both St. Michael's and St. Malachy's are presented on the laudable East New York project, linked here and here.