Noodles is taken to The NYS Reformatory For Boys. This side of the street was filmed in Flushing Avenue
in the Bedford Stuyvesant neighborhood in Brooklyn and the other side from where Max and the others
watch was filmed in Main Street Brooklyn, midway between Manhattan Bridge and Brooklyn Bridge.

From the movie

The building in Flushing Avenue was built in 1903-4, in the architectural style of a Medieval Fortress and originally owned by the Street Cleaning Dept. Depot, now Department of Sanitation/ Dept. of Environmental Protection. 

Architect: Warren & Wetmore, the same Beaux-Arts firm that gave us Grand Central Terminal, the NY Yacht Club and the Helmsley Building.

The NYS Reformatory for Boys in Once Upon A Time In America filmed in 1982

The Atlantic City Armory (CGI modified) from a 2011 episode (S02E08) of Boardwalk Empire

Recent street view on Google - approx. 2012

The gang watch as Noodles is taken to the reformatory and behind them is a wall with unusual lettering and windows. 

This is located on Main Street Brooklyn near to Plymouth Street - photo (2008)


It can also be on viewed on Google maps


These are the actual buildings on the other side of Main Street - photos (2008)