What could be the source of a leak on the passenger side under the dash on a 2000 Nissan Frontier?

Is the water cold? If so it is probably due to a condensate drain tube stuck closed. Look for the evaporator enclosure under hood. On the bottom there is a small rubber outlet that will allow condensation to escape. Sometimes they stick closed after a period of non-use. No need to replace it. Just manually open it up and maybe clean out the end a little bit.

I would guess that it is the windshield seals. Check them to see if you can find any gaps on the outside of the weatherstripping.