Amfleet,
There are several factors that can play into this, however as a general rule Superliner sleepers are usually cheaper than Viewliners.
First is simply the nature of the double decker car. There are more bedrooms in a Superliner than a Viewliner. So supply and demand dictates that prices for the more limited amount of bedrooms in a Viewliner would cost more. A Viewliner is easier to sell out than a Superliner, so you can charge more for the Viewliner rooms. Assuming that each train has two sleepers, then the Cap is running with 40 bedrooms, while the LSL has 27 bedrooms total.
Second is the fact that the LSL probably has a broader passenger base than does the Capital Limited. First of all there are two trains to choose from if one wants to go from DC to Chicago. Now while there are two from NY to CHI, they really serve two completely different markets. From Boston there is only one choice.
Next look at the list of cities served by the LSL by comparison to the Cap. Many of the stops on the LSL have much larger populations than do those on the Cap. This also makes it easier to sell out the train and again supply and demand says that you can therefore charge more.
The third factor is simply when are you traveling. If you priced the LSL out to CHI on a weekend, while returning on the Cap on a weekday, then that will affect prices. Also is there a holiday anywhere in there too? That will also influence the price.
Finally while there is no way for you to know what the current sell out rate for each train is, that will affect prices. If the LSL has met it's minimum sell points, then the prices go up. The Cap may not have hit it's minimum sell point.
There may even be a few other factors that I'm not aware of or thinking about at present.
Ps. IMHO while a Superliner Diner & Sightseer lounges are better than any thing in the single level fleet. However I do think that a Viewliner sleeper is far superior to a Superliner sleeper.