I remember Amtrak and VIA had a joint overnight run between NYP and Toronto for a year or two around 1994 that was called the Niagara Rainbow, but it didn't run as part of the Lake Shore. It ran weekends only, initially Friday and Saturday nights westbound and Saturday and Sunday nights eastbound, and later only Friday west and Sunday night east. It had a late night departure from NYP, about 10:30 p.m., and an eastbound arrival about 7 a.m. I believe it actually had a standard 10-6 heritage sleeper, but the rooms were available at the slumbercoach rate as an incentive to get people to try it. Alas, it ended before I had a chance to ride it.Those are the only two options I can think of. One iteration of the Niagara Rainbow was a Toronto slumbercoach and coach attached to the LSL, so there is precedent for same-train service to Boston with a change of cars.
The schedule seemed like it could have been handy for weekend travelers from New York to Rochester and Buffalo, as well as Toronto, and with that schedule one could easily have a Boston section that would have decent arrival and departure times there. And a Boston-Toronto routing through Albany would be much more direct than going all around through Portland, Sherbrooke and Montreal. But you'd still have to figure out the border-crossing issues. If the cost of a sleeper room is comparable to Amtrak's contemporary fares, I don't think the people who'd ride it would take kindly to having to pile off the train at 7 a.m. with all their luggage for an hour-long customs inspection at NFS.