I don't agree with the preceding. The bus is the slowest and most expensive option - other than a cab, which is REALLY expensive. I only recommend the limo-bus for those who have lots of luggage which is not the case on a quick layover visit. Just check the bags on through or leave at the luggage counter.

The Keisei Skyliner is faster and cheaper than the bus and the Keisei Rapid line even cheaper still. Just take it to either Nippori or Keisei-Ueno and change to either the Yamanote Loop Line or the subway to wherever you want to go. For a few hours, Asakusa is a good choice to visit, as is the Ueno Park area or Akihabara. If it is Sunday, try a connection to Harajuku. Asakusa is a quick 3 stops east of Ueno on the Ginza Line subway and provides a very nice visit with Senso-ji Temple complex and the Nakamise outdoor shopping arcade as well as the Sumida River-front park. Ueno Park is just steps from the Keisei-Ueno Station and has museums, temples and street performers. The Ame-Yoko shopping street is across the street. Akihabara "Electric Town" is 2 stops south of Ueno on the Hibya Line subway. Tokyo Station is several stops from Ueno or Nippori on the Yamanote Loop Line and is a short walk from the Imperial Palace. Be aware that Tokyo Station is huge, crowded and can be very confusing for first-timers.

I figure you will need a couple of hours to get through C&I, dump off the luggage and get some yen from an ATM or cash exchange counter. The train is another hour or so. You will want to start back to NRT at least 3 hours before your departure to allow 2 hours for check-in and security. That means you will have 5 to 6 hours actually in Tokyo. Find a good guidebook and pick a couple of destinations you wish to visit, figure on getting a meal at one of them and enjoy the visit. There are thousands of inexpensive restaurants in the side streets and around every tourist site.