I would at least get a one-way Suica & NEX package for 3,500 yen. This basically lets you ride the NEX into town for 2,000 yen instead of the usual 3,000 yen. The cheap train is something like 1,200 each way so you are basically paying a premium of 800 yen to get a reserved seat on a much less crowded train.

Off the top of my head I think you are talking about the Hundred Stay, which is the only hotel I know of in that area. You can take NEX to Shinjuku and then go one stop outbound on the Chuo local (yellow) line to Okubo, which will put you just down the street from the hotel.

If you buy the one-way Suica NEX pass you can use part of the Suica credit for the cheap train on the return to Narita, assuming you have any credit left after hopping around town. The outbound Keisei limited express should not be ridiculously crowded during the morning rush hour, whereas the inbound one could easily be. On the return I would catch the Keisei train at Ueno, where it starts. This requires a bit more walking and train riding but is more likely to guarantee you a seat.