Generally speaking, buses are the cheapest option, followed by planes then the Shinkansen.
The Shinkansen is a lot more convenient though since it dumps you right in the center of the city. Also a lot comfier.
Osaka <-> Tokyo by Shinkansen is around $160, but a plane ticket can cost less than a $100. The prices vary a lot more than the Shinkansen though. Also for the Shinkansen you can buy a ticket for an hour before without an increase in cost.