I don't know. San Antonio has had them from 1984 at least. If memory serves it was the only zoo to hold them back in the 1980's.
About 3 years ago i saw a pair of whooping cranes at milwaukee zoo but in a caged in aviary. The national zoo in D.C. seems to have a pair,but this exhibit seems to be the best.
San Antonio Zoo, Calgary Zoo, Smithsonian's National Zoo, Lowry Park Zoo (still have theirs?), Milwaukee Zoo and Zoo New England - Stone Zoo. International Crane Foundation also houses them as does Audubon's ACRES facility. There could be others but I am unsure of non-Zoo related facilities.
there's a nice article here from 2010 which runs through the history of whooping cranes in captivity (and includes European collections which held them, and their holding dates; both are slightly at odds with what is on Zootierliste, if there are any editors reading this...). http://digitalcommons.unl.edu/cgi/v...1&FORM=PORE#search="whooping crane captivity"
I believe Jacksonville Zoo still have them as well - I saw them there (and at Lowry Park) in late 2013. Lovely birds - and even more so for me as they were the last 'new' crane species I had left to see.