No web site that I know of.
It depends on
your FF program
airline flown
status level
class of travel

Just get busy with a spreadsheet

This post One World Distances has a list of some direct flights that exist (or did exist at that time it was done). These are flights with a single flight number. They may go via several airports.. Some even require a change of aircraft, like, MIA-NRT on AA, but they are a single flight number, which is the important thing

Flights between destinations are being reduced every day, with current world problems, so you need to check.

Distances from http://gc.kls2.com/ or from airline web sites