Train, Limousine bus, cabs are few options to arrive in Tokyo from Narita airport
Trains - Narita airport liner, Keisei liner, Yokosuka line, Keisei line are diff type of train options. Cheapest is the Yokosuka line or keisei line which are regular trains. If you take Narita express or Keisei liner these trains are fast and the tickets are around 3000 JPY.
These trains typically take you to Ueno - Shinjuku - Shibuya - SHinagawa - Tokyo - Yokohama as junctions.
Limousine Bus - These have more connectivity. The ticket price is roughly 3000 JPY. These take you to stations such as SHinjuku - Shinagawa etc as well as have connectivity to hotels in Shinjuku, Akasaka, SHinagawa, Shibuya, Ebisu so that you can choose the nearest place where you plan to go and then take a cab from there. There is a Tokyo City terminus center (TCAT) in Suitengumae and a Yokohama City Terminus (YCAT) which also act as central locations where the bus can take you and then you can take local train /cab / bus.
Shared Cabs - Earlier they used to have shared cabs. Now I dont know and hence you might want to check out.
Cabs - If it is urgent or fast, you might want to take a cab. SInce its a long haul you can try to negotiate as well. For eg. by meter say Akasaka - Narita can be around 18000 - 20000 JPY but one can try to negotiate at 16000 JPY or 18000 JPY flat. Since these are long trips, many times the drivers negotiate the same.
In all the above cases, you can get receipts and hence you can get it reimbursed from company in case of corporate travels.