Upon arriving at Narita, you can take the Narita Express (N'EX) directly to Tokyo Station. The N'EX is the most convenient option as it is fast (about an hour) and comfortable. Purchase your N'EX ticket at the airport. You can also use your Suica card to board, but purchasing a reserved seat might be more comfortable after a long flight. From Tokyo Station, you will take the Shinkansen (bullet train) to Kyoto Station. The most common services for this route are the Nozomi and Hikari trains. Nozomi is the fastest, taking about 2 hours and 20 minutes, but Hikari is only slightly slower. I would buy Shinkansen tickets in advance, especially if traveling during peak hours or on holidays...