I just rode the train this summer. You need to be in one of the open cars and seated on the right side as the train leaves Durango. Those are the odd numbered seats. I was in seat #1 in a car towards the rear of the train which was the very first seat on the right side of that car. My photos are posted here, do a search for Durango to find them and photos posted by others. I used a Nikon D700 and a 80-200 2.8. I just realized much of what I said was the same as Old Sea Dog said above. I didn't see his post before I wrote mine.

Oldseadog,
Tip 1; Try to get a seat on the right side of the coach. The train follows the Animas river and the opportunities are many. Tip 2;The high light reflections off the water will blow out unless you compensate. Tip3; I've always been happy with the food at Natalia's 1912 restaurant in Silverton (they have an out door patio, nice on a good day)
Have a good trip,enjoy

Edit; besides siitng on the right try for a coach towards the end of the train and if at all possible, the front set. Otherwise you stand a good chance of getting a picture of the person in front of you using their camera, in every one of your shots.

Been there, done that - Durange to Silverton and back. Shutter at 1/500 or faster as your camera allows. You can take a round trip or take a bus back. We did a round trip and found the return rather repetitious. I have seen images posted in UHH taken from the road but I don't think the bus stops for photoshoots. The images I saw were very nice landscapes of the mountainous country there. I know you'll enjoy the train ride. PS: The train stops for water for the engine at one point and may offer some interesting shots.

That should be a fantastic trip and I'm sure you'll enjoy it. I've seen but not ridden on the Durango & Silverton Train--I was once stopped by it for about ten minutes while if filled up and have nice pictures of that. I then rode my motorcycle down the canyon where the train runs--it is beautiful and you will have a lot of chances for fantastic pictures--more than I did on the bike. I have ridden old trains in Australia up to the Rainforest and out of San Diego from Campo to Tecate, Mexico and they are fun and provide a great chance for photos.

I agree with most of the advice given--you want to shoot fast enough to compensate for the train shake and movement and not much chance to steady your camera (I agree with the at least 1/500 minimum recommendation). If you're shooting just scenery you can probably get by with a lower F-stop but some of the best pictures will be of the train going around curves and then you'll want as much depth of field as you can get. If it's clear that should not be a big problem but I did find that when it's foggy it's more of a challenge but for the pictures that do come out it's a great opportunity so don't forego pictures if you run into fog. For the train pictures you should try to be as far back in the train as possible because the more you get the better the pictures.

The rest of your trip sounds fantastic too but be sure you have a sturdy vehicle going into Chaco Canyon. It's very interesting and has some really good photo opportunities but the road is not maintained. (If you have time to head west to Canyon de Chelly is well worth it. Take the guided tour into the canyon and you'll get some of the best photos imaginable. Both scenery and cliff-dwellings but also the birds--crows and raptors--gliding along the red cliffs are not to be missed. If you have a longer lens you'll want to take that for the birds--the birds casting shadows on the cliffs are some of my favorite pictures that I've taken.

Have a great trip and you'll have fun with picture taking at each spot.

I have ridden that train (and the Cumbres &Toltec Scenic RR *) many times. When I upgraded to a full frame SLR the lens I used was a 24-85. About a year ago I did a review of the images focusing on what settings I used most in an attempt to make a decision on a prime. I found that a vast majority of the time I was in the 24mm-44mm~ range. Your lens should work just fine, if you like the same type of images I do
The train moves at about 10 mph so you'll need a fast 1/500 or faster shutter speed depending on conditions of course.
*My preference for whatever that might be worth

I took that trip about 37 years ago. You'll never forget it. You'll need a fast shutter speed(250 or above) and probably an aperture of F8 or higher. If I had to choose one over the other it would be shutter speed. The gondola car in the back is a good place to be if it's not raining. You can get a great shot of the engine and tender going around a sharp curve against the mountain from the right side. The river is mostly on the right side also. I remember an old watering tank on the left side that's neat. I've been on several of these train trips since I took this one. This one is my favorite.