Joe,
I can't speak to Durango since I don't have much recent experience there, but for restaurants near the C&TS, your choices can be a bit limited and depend on the day of the week.
As others have said, Chama and Antonito are small towns, particularly Antonito. There are two restaurants on the main drag in Antonito that I have patronized. The Dutch Mill has been mentioned. That is where I go for breakfast when in town for Friends Work Sessions. That's where the locals hang out; they show up for coffee around 6:30am which is half an hour before the cook shows up, but there always seems to be someone there already to have the coffee brewing (FYI, one of the locals is an elderly gentleman who parachuted into Normandy on D-Day). For dinner I usually ended up going to Dos Hermanas just up the street. As you might expect, they serve good Mexican food.
In Chama, there is a bit more choice. The High Country south of town has been mentioned. Their draw is that they are open every day, but there have ben changes of ownership and many say the quality has gone down hill. Besides the Subway already mentioned, Foster's is the only restaurant in town that is consistently open, but they can be crowded and that can make the service very slow. The Box Car is a generally better choice, and they have outdoor seating, but they are not open for dinner Sunday-Tuesday.
The Elkhorn used to serve dinner - and it was good - but as of last year they only do breakfast and lunch. The word is they have not been able to get a cook to handle dinner (I guess that's one of the drawbacks in being in an area with a limited labor pool).
Finally, as mentioned, for breakfast, Fina's (across the street from High Country) does breakfast and lunch. They open at 6am and that is where many of the locals, including some of the train crew, have breakfast. As a sidelight, if the fella who brings you your menu has a trim grey mustache and sports a straw stetson (and is packing a pistol) that's probably Billy Elbrock, a member of the C&TS Commission and Mayor of Chama.
Hope that helps.
Rob