We will be getting our passes in December. But here is the thing we are taking the skyliner from Narita to Ueno then have to get on the Joetsu to Niigata. So should we go ahead and go to the counter at the Narita airport to activate our pass or do it at the station in Ueno?
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http://www.japanrailpass.net/en/exchange.html
You should first make sure you will be there when the office is open. If that is not an issue, you can do it at either, but there may be a lot of people trying to activate their passes at Narita. It is up to you.
The Narita office can get very busy, with a lot travellers trying to activate their passes as soon as they arrive in Japan. If you don't mind queueing and have the time to wait, then of course you can activate your pass there. See if there's a long line when you arrive and decide then! If so, we would probably recommend waiting until you get to Ueno and activating it there.
As Tenjin said, please be sure to check the opening hours of the exchange offices!
Japan Experience