However, the Shinagawa to Akihabara run on the Yamanote Line *will* be very crowded on a weekday morning.

Another option is to stay around Tokyo Station. There is a regular JR bus service from the Yaesu side (east side) of the station to Tsukuba, which stops at several places in the Tsukuba area. It takes about an hour and costs 900 - 1,200 yen, but you get a guaranteed seat.