I just started watching it on Netflix. I watched the first two episodes (an extended pilot), and I was surprised/pleased at just how much they featured Amtrak.
Part of me wonders if that was Angela Lansbury, the writers, or a bit of both. In a couple of scenes, someone offers to book a flight or car for her, and she waves them off and says, "Oh, no. I'm perfectly fine on the train," and, "Nonsense. I'll take a train." You get a sense it's her favorite way to travel.
The logo was clearly visible on the side of the train in almost every shot, and there was a scene on the train in which it appeared Jessica was sitting in BC (the seats were leather). You could see the seat numbers, seat checks, etc.
I'm not sure which train she was on. The cars looked like Amcans, and she was supposedly leaving NYC, but the tracks were above-ground. She's from Maine, but she told the conductor to just "check her bags through to Boston and [she'd] pick them up there," when she had to run off of that train and catch a different one (to solve the murder, of course!)