Touchy situation.
MY OPINION would be, tell him in private what you think. GIVE him a real one to smoke. Explain to him where to buy legit cigars.
This is a safe approach. I would not tell them they were fake unless asked directly what I thought about the cigars. Direct questions should have direct answers and lip service does no one good.
You may suggest that the next time he is Cuba to go to the a particular place to buy, or suggest a cigar that is unlikely to be faked. Mention that custom rolled cigars are available at a couple of hotels. "As much as I enjoy those Cohibas, I think bringing back some Cuaba Diademas, Monte A's, Sancho Sanchos... would be a real hoot and you may like them even more..." Something on those lines may work without pulling his card.
I got beat once on a box of Esplendidos that was bought in Cuba. Sure, they were "Cuban", the box, and perhaps the bands were real, but that was it. The tobacco was not bad and had triple cap, but were tight and not up the Cohiba level. Well, they were donated to the our troops in the Gulf region.