which city is a must to visitDepends on your personal preference! Sapporo is by far Hokkaido's biggest city. If you like big cities, make sure to head there.
Is it a good idea to take JR train from tokyo to hokaido?
A night train is a nice way to get from Tokyo to Hokkaido, but it is expensive. Flying is fastest and cheapest:
http://www.japan-guide.com/e/e5306.html
Mid Nov to early Dec good time to visit hokaido?
Frankly speaking, it is not the best time to visit. Winter is only about to start and the weather tends to be unstable. But it can still be enjoyable.