You need to convert them with ddconvert to be able to play them on MAME.
https://github.com/Happy-yappH/ddconvert
You can download the Windows binary in the downloads section.

If you have GCC, just do "gcc ddconvert.c". It works on any OS.
It makes an executable named "a" (with the proper extension on Windows).

Use a Command Line Interface and convert the dumps like this:
ddconvert [Original Dump File Path] [Converted Dump File Path]

Replace the respectives [ ] with what it asks (without the [ ] ).

Download the latest version of MAME/MESS.
Install it, and then get n64.zip and n64dd.zip ROMS.
Put those zips in "roms" folder (you don't need to extract anything, just put the zips).

Then, with a Command Line Interface (or a batch file):
To play just the disk:
mame n64dd -hard [PATH TO CONVERTED DISK FILE]
If you want to play a cart + disk combo (Like F-Zero X + Expansion Kit):
mame n64dd -cart [PATH TO N64 CARTRIDGE] -hard [PATH TO CONVERTED DISK FILE]

And if you want to only play a N64 game:
mame n64 -cart [PATH TO N64 CARTRIDGE]