There are two (identical) bus services to and from Tokyo.
The time to go between Tokyo Main Station and Tsukuba Station is about 2 hours. A timetable with both companys can be found here.
Discount tickets for the route Tsukuba to Tokyo are available at a vending machine in Dayz Town, in front of the Daiso. If your a travelling alone, these discount tickets are the cheapest option to go from Tsukuba to Tokyo, cheaper than the Tsukuba express discount tickets. It takes longer though. However in a group of 3 people, the discount ticket sold at the vending machine at the main bus station is cheaper.
Going back from Tokyo to Tsukuba, it is cheaper to use the Tsukuba Express with a discount ticket than the bus tickets sold in Tokyo main station.