In the 1874 RLDS edition, the plural waves was replaced with the singular wave. The resulting phraseology, “upon the wave of the sea before the wind”, uses only singular noun forms and could be considered poetic. Nonetheless, the change was probably unintended; and the subsequent RLDS edition (in 1892) restored the original plural waves. Note that the following verse has the plural:
In fact, there is no instance of the singular wave in the entire Book of Mormon, only waves (eight of them in all, including here in Ether 6:5).
Summary: Maintain the plural waves in Ether 6:5 (and elsewhere in the text).