5 day stopover in Japan on way back to US

I'm traveling with 2 sons, 18 & 20 back to USA from Manila thru Narita. Was hoping to do a 5 day stopover in Japan. They would like to see Tokyo/Fish Market and I would like to see Kyoto. Any itinerary suggestions? Transportation? How much $ for food and hotel? We've never been to Japan.

What exact dates and times are your flights?

They would like to see Tokyo/Fish Market

Tokyo
http://www.japan-guide.com/e/e2164.html
Tsukiji
http://www.japan-guide.com/e/e3021.html

and I would like to see Kyoto.

http://www.japan-guide.com/e/e2158.html
http://www.japan-guide.com/e/e2363.html

Any itinerary suggestions?

Depends on the above but 3 days Tokyo, 2 days Kyoto

Transportation?

I'd probably buy a 7-day JR Pass and use the Shinkansen ("Bullet trains")
http://www.japan-guide.com/e/e2361.html

How much $ for food and hotel?

Japan travel budgets
http://www.japan-guide.com/e/e2410.html

Tokyo Hotel and area guide
http://www.japan-guide.com/hotels/tokyo.html

Triples may not always be easy to find so you may prefer to split up rooms, or try Japanese style accommodation in Ryokan/Minshuku which can often handle three per room.

Enjoy your trip!