Getting started and general outline

You don't give a lot of info, such as how many days total your planned trip will be, but your first part of your trip would be hard on you if not completely excruciating. To go from Tokyo to Sapporo takes over 9 hours and will completely kill a whole day for you. So, you have a few choices:
1) Stop somewhere along the way. Even if you don't want to see anything in Honshu north of Tokyo, you could get to Hakodate in about 5½ hours and still see something. Then the next day proceed to Sapporo and use it as a home base.

2) Fly to Sapporo and back. You can get a cheap ticket from a low cost carrier like Jet Star for as low as ¥4190 yen per person and get there in about 2 hours. You could then still have the day to go sightseeing, and on the way back, fly down to Kansai (Kyoto, Osaka, Nara) for nearly the same fare. Another cheap fare is ANA's Experience Japan Fare. You could then use a JR Pass to expand your trip a bit, like go see Hiroshima or Takayama, and still make it worth the cost of the pass as you travel north to Tokyo.
Since you are already seeing Tokyo, you can largely skip Osaka during the daytime. But at night the city comes alive and has some great places to see, such as Dotonbori, plus the night views from the Umeda Sky Bldg, and Abeno Harukas Bldg are terrific. You can see Osaka after you see the temples and shrines in Kyoto, which close around 5 PM.

There are many nearby sights for you to enjoy, including Himeji, Koyasan, Hikone, and Kobe.

Thank you so much for the reply!
Here are some more info on the trip:
We are staying for 14 days and landing at 10 pm in Tokyo on our first night. So one of our options is to stay overnight, wake up early the following day to see the fish market, then depart for Sapporo. We are now searching for a flight from Tokyo to Sapporo as that seems like the most reasonable plan (time > a few dollars in this situation). From there, the trip gets much simpler as we will be visiting the more popular areas such as Osaka, Kyoto, and Nara.
Again, thank you for the showing us different options!

Hi,
Wow...well you don't say where you are flying into Japan from, but it'll take you 45-60 minutes upon landing to get your bags and go through Immigration/Customs, plus an hour to get into Tokyo. To see the Tsukiji Fish Market - you can see it here these days, they only take 2 groups of 60 people and people rush to get in line for the tours from 4:30 AM - by 5 AM you may be too late. At that hour you'd also probably have to take a taxi. So after flying across the world and getting a couple of hours of sleep, to rush over to Tsukiji is either quite enthusiastic...or you're a glutton for suffering. But you won't see any place like Tsukiji in the whole world.

For Hokkaido, check this info on what to see and do:

http://en.visit-hokkaido.jp/

Enjoy your trip!