It's what the airlines would call congestion pricing. You charge more for the more popular route, which you know is easy to sell out. The Lake Shore is far more likely to sell out in Feb, than is the Zephyr. The Lake Shore, unlike the Zephyr, does tend to carry some business people who don't need to rush (i.e. fly) to Chicago from NY. However, most business people can't take two plus days to get from Chicago to California.
Secondly the Lake Shore carries far less deluxe bedrooms than does the Zephyr, since it utilizes Viewliner equipment. Even during the peak months when the LSL has two sleepers out of NY and one out of Boston, it only has a total of 6 deluxe rooms. Typically during the winter the LSL only runs with 1 sleeper out of NY, which reduces that total of 6 deluxe to 4.
The Zephyr, which runs with two sleeper cars in the winter carries a total of 10 deluxe bedrooms, since it utilizes Superliner equipment.
So with higher ridership and less deluxe rooms, the LSL demands a premium for it's deluxe rooms.