Here is what I have gleaned about Thompson boatbuilders from;
"The Boat Builders of Hamilton (From the mid 1800's to the present)" by Laura Edith Baldwin, 1992, Pub: In Harmony Promotions (54 pages)
John Thompson (born?) was apparently the first in line of a family of starcrossed, boatbuilders who built a boat called the Pal 16. John drowned May 24th, 1887 off Dyne's Hotel (a historic tavern on Lake Ontario, which was recently torn down in contravention of a historic preservation order).
His son James (born?) carried on the family business. The author, Laura Baldwin "recalls hearing her parents speak of the drowning which took the lives of most of the Thompson family". Somewhat ambiguously, "James has the sad distinction of being the sole survivor of a drowning in the (Hamilton) bay which took most of his family".
James Thompson bought the 13 boathouses at the foot of Bay Street owned by James Massie in the 1920's and lived into his 90's.
A group calling itself the "Pal's Yacht Club met in the loft of the Thompson boathouse, which was later used by a group of Sea Cadets".
Bob Thompson, a onetime commodore of the Royal Hamilton Yacht Club was the great grandson of founder John Thompson. He convened a group called the Shellback Club in 1987 which met twice monthly for lunch to hear a speaker about topics relating to their common interests in boats and the bay.
There is a diagram of the location of 11 boathouses reprinted from "A Mountain and a City", by Marjorie Freeman Campbell. As it isn't particularly clear, I'll try to get a copy from the original book.