I imagine these could be the stones to which the Rev. refers - there are two of them, and they are on the way home to Breachacha castle (the Macleans' abode) from Grishipoll. But let me know if you know better.
Finding our labour [on Grishipoll cairn] ineffectual, we left our work, and returned to Mr. M's house. In our road, I saw several upright stones, particularly two, called the whispering stones*, which they call the giant's grave, and also evident traces of ancient cairns; all of which, though hardly noticed by or known to the natives, bear strong marks of monumental labour.
*So called from a silly trick, practised by the natives, of placing a person behind one of the stones, pretending he may hear what is whispered at the other, and having thus stationed him, he is left a dupe to his own credulity.
The Reverend Clarke sounds like The biggest cynic of all time - he can't even believe in other people's belief?
From p235 of 'The Life and Remains of the Rev. Edward Daniel Clarke' (a professor of mineralogy at Cambridge) by William Otter (1824) - viewable on Google Books. He visited Coll in 1797.
Coflein says the stones were known as 'Na Sgialaichean' in 1937 and still in 1972 (what is the translation?). They were by tradition "ancient burial marks". They are 46 feet apart; one is 5 ft tall, the other 6.