Fresno these days is oriented more at freeways than railroads, and there are a lot of areas you really don't want to stay or be in, but some Googling suggests:

- Holiday Inn Express & Hampton Inn near Herndon Ave. (can see UP from upper floors on the NE side)
- Picadilly Inn West Shaw (can't see BNSF from the Inn, but it's a short walk from the W. Shaw & N. Marks grade separations)
- The dives in the red-light district along N. Golden State between Olive & Clinton (across the street from UP) seem to be mostly abandoned, probably sold to HSR or in the process, but if you feel like paying by the hour...
- Fresno Community Hospital? No, you don't want to stay there, but it's a block from BNSF.

If you're interested in UP, there might be closer offerings in Madera, where the freeway and the tracks are pretty close. Lodging seems to almost deliberately avoid BNSF. Otherwise, you're probably looking at lodging near a freeway or in commercial areas (Woodward Park, E. Shaw near Fresno State, perhaps a couple of remaining places on Blackstone that haven't gone hourly), and commuting by car to fanning sites.