A strain is a subset of a species, differentiated by slight physical characteristics. For example, the Horn Lake strain has a white tip to its dorsal fin, and males are a deep red along the belly and often have a hump back and hook jaw.
The DEC will supply you with both a list of reclaimed ponds as well as those stocked with heritage strains. I watch them closely and fish a lot of them.
Here are a few:
Burge Pond, Horseshoe Pond and Crab Pond in the Pharoah Lake Wilderness are stocked with the Little Tupper Lake Strain of brook trout, as is Challis Pond in the nearby Hammond Pond Wild Forest.
Mountain Pond and Dry Lake in the St. Regis Canoe Area are stocked with the Little Tupper Lake Strain, while Nellie and Bessie Pond (also in the Canoe Area) have Horn Lake strain.
Mountain Pond, Black Pond and Long Pond, all wild forest ponds in the Town of Brighton, Franklin County, have Windfall Pond strain. Nearby Whey Pond in the Saranac Lake Wild Forest also has Windfall Pond strain.