This item of recent history is surprisingly hard to pin down, as the following NY Times article illustrates:

http://www.nytimes.com/2003/07/26/opinion/did-he-bang-it-nikita-khrushchev-and-the-shoe.html

Of related interest, people often conflate this event with his famous utterance "we will bury you", which was said at the Polish embassy in Moscow. People often take the dramatic shoe banging and this phrase together in one act, but they were separate and as you point out there is no clear answer about whether in fact he did bang his shoe on the lectern.