How do the 3 sannin know about using Five Elements Seal on Naruto?
Apparently so. It's possible that other people were able to use the seal (for instance, Kushina, who was a sealing expert, or the Second and First Hokages, who knew advanced sealing techniques, but passed away).

It's possible that they referred to only living shinobi for that purpose (it makes sense, because they were trying to figure out who unsealed it).

I believe the technique was passed down to (or invented by) the Third, and he in turn taught it to his disciples.

Note that Minato never used the Five Element Seal.