Top three are the CZ, CS, and EB. After that it’s a toss up, and it comes down to what you like. I’ve written my opinions on the routes I’ve been on excluding the CZ.
Although I’ve never been on it, the CZ wins for me. It has mountains, canyons, fields, desert, even a bit of the San Pablo bay.
After that I’d say the CS. The ocean is beautiful and you can go dolphin watching from the train, and the Cascades are also pretty nice, but I’d say donner pass offers better scenery. Although in Northern California the scenery is actually very beautiful, and I’ve been able to see much of it in daylight twice. However the Salinas valley is very boring in my opinion, and I’m sure parts of Oregon and Washington can be blring for some when you’re used to it.
The Empire Builder has its highlights, the cascades, the Columbia River Gorge, glacier, and the Midwest. But for a lot of the route, big sky country, it gets boring real fast and IIRC service is limited in that section, and if it’s snowy then you’re literally seeing the same thing for the whole day.
The SWC is pleasant, glorieta and Raton pass are nice. However personally the true beauty of the route is/was the history to it, which is/was the semaphores, wig wag, and large sections of jointed rail. It can get a bit boring sometimes.
Sunset Limited, well, I don’t remember the scenery east of San Antonio. But the scenery west is just desert. Personally that’s not anything too interesting to me.
I’ve ridden the full route of the Texas Eagle once, I found the scenery pleasant. Although I’m not sure I’d still be too interested after a handful of rides.
On the Cardinal, the scenery was nice. During the scenic highlight of the new River Gorge there was a wall of trees obstructing the view for most of it, which hindered the ability to really enjoy it. The city skylines were nice as well though.
The Empire Service had good scenery, although personally I prefer mountain ranges where the train is truly going through in it like the CS and EB.
On the NEC, the New England scenery was pleasant, so were the city views.