I've now had a reply from The Watt Library and it does sound like Major Bonar's Home may not have been Bank Top House, The Library said:
"Thank you for your recent enquiry to The Watt Library. Bank Top House was also known as The Working Boys' Home and was a home for "Destitute and Homeless working lads over 14". The Home first appears in the Greenock Post Office Directory in 1876/77 and was then at 5 Bogle Street. It was begun in connection with the Greenock Working Boys' and Girls' Religious Society who held meetings in the Society's committee rooms at 46 Cathcart Street and Mission Hall, Broad Close.
I believe this is different from the Industrial Schools, these were more like homes for wayward boys or boys who had been in trouble and were sent there by the Sheriff.
Unfortunately, this library does not hold any records for the Home, they may not have survived. You might try The Mitchell Library in Glasgow or The National Archives in Edinburgh."
Alistair