This article from the New York Times won’t give you a definitive answer, but it does provide interesting background on the differences between the standard English (GO-doh), American (go-DOH), and French (GO-DOH, equal emphasis) pronunciations of the elusive Godot.
Interestingly, the notoriously finicky Beckett Estate has no position on how the word should be pronounced. While there are reports that Beckett preferred first syllable emphasis, his writings never specify how ‘Godot’ should be pronounced, and there are no recordings of him saying the word. Maybe someday we’ll find out what Beckett really intended. Until then, we’ll just have to wait…
Source: New York Times