another option instead of narita express is the airport limousine bus which can get you right to your hotel depending on where you are staying. they will assist with luggage and then you don't have to bother storing it. http://www.limousinebus.co.jp/en/ and they also don't require a potential transfer on the train/subway system.

As for where to stay, you should consider what are your priorities. For example, on one trip I stayed in Shinjuku and it was fun because it was madness outside with lots going on. On other trips, i've stayed in quieter parts of town but right next to a train station.

If price is the first consideration, perhaps narrow down the possibilities and then evaluate whether you want to stay in the thick of things like in Shinjuku or Shibuya or perhaps you might be happier with something calmer but easily accessible to the excitement.

You'll have an awesome regardless - tokyo is a blast. I'm heading back this fall for what is turning out to be an annual trip!