If you're flexible enough to play an N64 game using a keyboard, you should have no problem adapting to something like an Xbox 360/One controller.
The dongle to allow any standard X360/One controller to pair to your PC instead of a console is affordable and can easily be ordered online, and the X360/One both have enough face buttons and shoulder buttons to do a capable job when you remap the N64 controller onto them.
My suggestion would be to have Left/Right Bumper mapped to L/R since they're digital controls, and remap either LT or RT onto Z, since it was intended as a trigger control. Map the N64's A and B onto the controller's A and X buttons respectively, map the D-pad 1:1, use the left stick as the analog stick, and find a way of mapping the right stick onto C-Up, C-Left, and C-Down. Map Start onto, well, Start, and you're good to go.