What is the best way (cheapest, quickest) from Narita Airport to Tsukuba?
There's actually only one sane way to make this trip: take the direct bus from the airport to Tsukuba for 2200 yen. Buses run hourly and take ~60 minutes, schedules here: http://pfwww.kek.jp/users_info/access/busnrte.html
All other options either involve a massive detour via Tokyo, doubling the travel time, or are wildly expensive (taxi).
There actually is another (but less sane) way to travel, and is preferable if you want to avoid the bus. Here it is:
Keisei Sky Access Line to Higashi-Matsudo;
JR Musashino Line to Minami-Nagayama;
Tsukuba Express to Tsukuba.