Not so much a replacement for as an additional. The idea was to have excess capacity so each of the aqueducts could be brought down for inspection and repair. After a century, it's a really good plan.
The aqueduct system into NYC is really amazing. They start in the Catskills, which are on the other side of the Hudson River from NYC, so must cross (under) the river. IIRC, they're on the order of 30' in diameter (cue the Die Hard reruns).