Montreal is not large city like Paris and New York, nor a important place in aviation history like Kitty Hawk(Wright brothers first flight) or Friedrichshafen (Zeppelin airship first flight). Why Montreal is being chosen as the headquarters of 2 biggest aviation organization.
ICAO is headquartered in Montreal because that was the result of a vote by the founding members (PICAO is Provisional ICAO):
Why was Montreal selected? While insisting on the excellent hospitality offered since of the beginnings of PICAO by the federal, provincial and municipal authorities, the delegates described Montreal like a roundabout of the international means of communication and a strategic centre with a formidable economic, scientific, technical and aeronautical expansion being felt for a few years. One insisted on the vast spaces of the Canadian territory, offering unlimited possibilities for the scientific and practical experiments in the field of aviation. Moreover, PICAO was to be established as close as possible to the central head office of the United Nations.
And IATA is in Montreal because its founding statutes said that it must be in the same location as ICAO:
Article II of the IATA 1945 Statutes states that “The Head Office of this Association shall be maintained in the city in which the headquarters of the International Civil Aviation Organization is located.”; this article was later amended to leave an opening for a possible other place as determined by the General Meeting
In addition to Pondlife's answer, it may be worth noting that Montreal is an important place in aviation history as the Convention for the Unification of Certain Rules for International Carriage by Air (now known as the Montreal Convention) was signed there.