For the N'ex, Shinjuku is the only option that allows you to change only once. Change to the Oedo line in Shinjuku. Due to the N'ex following the loop around Tokyo it is a timewise long option. Other options will have two changes. The easiest is change at Tokyo to the Marunouchi line, and again at Kasumigaseki to the Hibiya line.

If you want to try the Keisei Skyliner, that can be done with one change at Ueno, and it is the fastests of the train all the way options.