when will your plane arrived Narita? will you arrive shinagawa JR before 3pm (there are shuttle bus in every 20 mins after 3pm)? Other toyoko inn also provides twin rooms (110cm wide) but just not as spacious as the deluxe twin 天王洲 (140cm wide beds with living room area).
If no shuttle bus, you can take narita express to Tokyo/Shinagawa or skyliner, then take 山手線 to 浜松町 and transfer to monorail to 天王洲. It seems a bit complicated if you don't take shuttle bus. Otherwise, Narita express to Shinagawa and then shuttle bus to hotel would be a good choice (even if you live in Shinjuku, you also need to transfer to 山手線 and the inn is not close to JR station).
You may also consider Hotel Gracery (Gorzilla hotel). I asked before and kids under 12 can stay free with parents if no extra bedding required. However, the rate must be higher than Toyoko inn.