Transportation: What is the best way to get from Narita Airport to Tsukuba?

Actually, there is only one sensible way to make this trip: take the direct bus from the airport to Tsukuba for 2200 yen. The buses leave every hour and last about 60 minutes, the schedules are here:

All other options involve a massive detour through Tokyo, doubling the travel time, or are extremely expensive (taxi).