Church of the Covenant, an 1867 Gothic Revival masterpiece, has one of the largest collections of liturgical windows by Louis Comfort Tiffany in the country; its 236 foot steeple is the tallest in Boston
I've visited the 9/11 Memorial a couple of times so skipped it on this trip; One World Trade Center (ie Freedom Tower) is still jaw-dropping as the tallest building in the Western Hemisphere (the same architect designed Willis Tower and Burj Khalifa)
I wanted to stop at the World Famous Crochet Museum for Mike but, unfortunately, it wasn't open; the former Fotomat booth is stuffed with all sorts of crocheted pieces