According to the Portcities website, the Lower Manor House stood very near the corner of Rotherhithe New Road with Lower Road, also near today's Rotherhithe Old Road. This is now the notorious one-way system, and one of the most congested parts of Rotherhithe, but it was very rural when Yates painted the house in 1826, and very isolated. Its nearest neighbour was a windmill. Later, it would have been located near to the St Helena's Gardens and Tavern. The 1843 B.R. Davies Map shows a possible candidate for Lower Manor House, and at that time the entire area was still very rural with market gardens and orchards. The house was still standing by the mid to late 1860s, but there is no sign of what happened to it at that point. Looking at the 1868 Ordnance Survey map of the area, which doesn't record a building of this shape in this sort of garden space, I suspect that it was demolished for low cost housing, which was swarming through the area at that time and eventually consumed the well known St Helena's Gardens (which was still open in 1868, but was right on the edge of the new housing developments, and was completely built over by 1914).
If anyone has any information about this building, and who owned it, please let me know. It would be great to know more about George Yates too. If anyone has any information, my email address is in the header at the top of the blog.