Train is almost surely the winner.

The train leaves from Tokyo station, arrives in Kyoto station. Simple.

Plane leaves from Haneda, and most flights arrive at Itami airport. From Itami, you get to Kyoto by airport bus (about 70 minutes). A taxi would cost in excess of $200. A few flights from Haneda go to Kansai airport (KIX), and from KIX you can take the 75-minute train to Kyoto station.

Train almost certainly wins on comfort, convenience, and probably price.