Travel to/back Sapporo and Tokyo

What is the fastest way to travel from Sapporo to Tokyo and and back? how?

It is a 90 minute flight. More details can be found here:
https://www.japan-guide.com/e/e5306.html

It's like a 9 hour train trek using the fastest trains.

You'll want to fly if you can.

90 minutes from Tokyo to New Chitose airport as a flight time, but add on all the rest of the drama of flying.
Add on time to get to the airport in Tokyo, check in, do the flight, collect bags and then get from New Chitose to Sapporo, and that's maybe four hours. Still less than half the time required by train.

It can be done in 3-3½ hours total if flying from Haneda. Domestic flights are like clockwork in Japan, it would hard to imagine anyone making it more efficient. I see people boarding the flight even 10 minutes before departure (not that I recommend that). And even have the luggage on the carousel before you deplane and make it to the baggage claim (which has far less than international flights).
There are some dirt cheap airfares for foreign tourists like ANA's Experience Japan Fare.
http://ana.ms/20Xtf8t
You could possibly get a cheaper fare on a LCC like Jet Star or Peach, but their cheaper fares are usually for more inconvenient flight times, plus you'd have to go to Narita, not to mention they have very stingy baggage allowances compared to the main carriers.