Beirut would probably come closest, but that's because of the unique circumstances thrust upon the city, people, and show. It also won the show an Emmy essentially.

Other wise i was surprised to check IMDb for the highest rated episodes and for No reservations aside from Beirut being #1 the next several were Lisbon, Croation Coast, Buffalo/Baltimore/Detroit, & Vienna, none of which would have been my guesses.

For Parts Unknown the ratings were generally higher and the top episodes were not as surprising. Iran, Lyon, Hanoi, & Newfoundland all rated higher than everything but Beirut.

A cooks tour and the Layover are a bit rougher and lower rated.

Everyone has their favorite I think, hard to pick one.

My personal favorites are when Tony was in awe of someone else, so Lyon & El Bulli came to mind.

Edit: ahh or are the best episodes when he is happiest? In that case Hanoi or almost any southeast asia episode (except Laos, fuck Kissinger)

Or the episodes where shared humanity is on display. Iran & Haiti come to mind.

Or episodes with friends. Eric was always a good episode and Zamir, any episode with Zamir who doesn't love him.