I just thought about one more option.
You could go up to Furano in one day (by Shinkansen and train), the next day visit the Farm and after that head to Tomakomai. From there take the Ferry to Hachinohe where you would arrive in the morning. In Hachinohe hopp on the Shinkansen and zipp back to Tokyo.
I actually think that the airfare to Sapporo will be around the same as the shinkansen/ltd. express anyway, i just thought you might plan to buy an Railpass
A quick check on
Enter the station name showed me a trip from Tokyo station to Furano in 5hours 24 min for 26 030 yen.
The same with a Shinkansen/ltd express combination will take 12 hours 35 min and cost 24 210yen. So its definetly worth to try to fly. it will cost you around 1000$ for the 2 of you if you dont have a railpass (a 7 day pass is around 28 000 yen per Person so roughly 600$ for a 7 day all Japan free pass for the 2 off you (like said before you would have to pay the sleeper train extra))
Firebird