Per popular request, I am pasting the pertinent parts of my reply to pianocat:
On the subject of hotels, there are two older places in the central downtown area, both are only one or two blocks from the railroad station. There is the Monte Vista, which dates from around 1927, which is decent but on the funky side. I have stayed there twice in their more basic rooms, and it was OK, but not my favorite. One block west is another historic structure, the Weatherford. I have not stayed there, but have taken a tour of the building. There are a limited number of hotel rooms, which are rather charming and have character. They do advise guests that it is an entertainment hotel and subject to late evening loud music. The same could be said for the Monte Vista. There is a plethora of restaurants in downtown Flagstaff.
The closest lodging to the station is the Rodeway Inn, which I stayed in once under a previous name, and it left something to be desired. It is convenient and cheap but gets poor reviews on Tripadvisor. ( I think they should tear the place down and improve the intersection. ) It is on Route 66, one block west of the west end of the station.
Within about five blocks of the station, adjacent to the Northern Arizona University campus, is the Drury Inn, a modern hotel, which I used to stay in, which is pretty nice. It is walkable, but is a rather dark walk at night and you might prefer a taxi to get there.
I no longer stay in Flagstaff lodgings, since I have a home here, but my favorite place is the Inn at 410, on Leroux Street, about five blocks north of the station, up a modest hill, just outside of the business district. I consider this the best place to stay in Flagstaff - very classy. I just punched up rates for July 15, and some of the rooms were $170. However, on one or two occasions, and this was at least three years ago, the owner, Gordon Watkins, gave me a rate of something like $125 or $150 if I paid cash. You might call them personally and say a friend told you this and see what may be offered. The office closes at 5pm, and guests arriving late must arrange this and they will leave the keys by the front door. I do like that place, although I see it is now for sale.
Additional comments:
The two other major hotels are the Hilton Doubletree and Little America, which are not in the immediate downtown area. These would be difficult without a car. A taxi would be needed to reach these. Many other motel possibilities, some good, some awful. Check Tripadvisor.
On the subject of restaurants, we have many, too numerous to mention. For middle of the road good grub, the most successful restaurant in town is Beaver Street Brewery, two short blocks south of the west end of the station platform. I am a frequent customer there after choir rehearsals.
For fine dining: All of these are within walking distance in the downtown area:
Cottage Place, a few doors west of Beaver Street Brewery. Excellent, but pricy cuisine. You get what you pay for. Most agree the finest place in town. ( in small bungalow- like having dinner at Grandma's house. )
Pasto, Italian restaurant with fine cuisine on Aspen Street.
Criollo, South American cuisine on North San Francisco, very near the station.
Karma Sushi, on Route 66 across from the station.
Streetside Saigon, moderately priced Vietnamese cuisine, on South San Francisco St., about three block south of the east end of station platform.
Josephine's Modern American Bistro on North Humphreys St. Upscale cuisine in historic Flagstaff bungalow house.
Brix, on North San Francsico just above business district. ( it backs up against the Inn at 410 ) Upscale, excellent food.
Many more moderate choices exist. You won't go hungry!
Flagstaff does have a local bus service, which I have yet to sample. There are a number of routes, but the service is more suited to local residents and students, and does not run late at night.