Well in my opinion at least, on the Lake Shore the right side of the train headed east, is the best. You can see part of the Erie Canal in upper NY State if you are on the right. Then south of Albany you have a great view of the Hudson River, West Point, and the Palisades. Again that would all be on the right side of the train.
The Great Lakes are on the left side of the train, however thanks to the times that you are in this area you won't see much, even if you are awake.
As for the Cardinal heading west, again you would want the right side. This will afford you the best views of the New River Gorge. The gorge is the highlight of this trip; there are some fantastic views in the gorge. Much of the gorge can only be seen by either train or by boating down the river. After that any side has decent scenery.
Connecticut Inland Route and Albany - Boston Corridor (Compass Service)
