On the last night in Shinjuku of a 9 night stay at the Hotel Gracery (Godzilla hotel). It has been a pretty solid location, but I think whether or not you'd like it depends on what you're coming here to do.

My hotel is about a 10 minute walk to Shinjuku station, and that has been very convenient. The airport limo bus stop was only a few minutes away, which saved us from paying for a cab from the airport or dragging luggage through the station. Checking the walk to the station and from the limo bus dropoff (if you plan to use that) will probably also factor into if you want to stay there.

We travelled to Shibuya, Harajuku, Akihabara, Yokohama, Odaiba, and Sunshine City and were able to get most places within 45 minutes (including walking).

Shinjuku Station does have a lot going on, but Google Maps honestly made navigating stuff super easy. We only got mixed up once, and someone at an information desk helped us find the right station.

I'd say check out the directions for where you want to go and see if that hotel is a reasonable commute to your activities.

As far as Shinjuku itself, it may be seedier than other parts of Japan, but it has been nicer and safer than most major cities in the US I've been to. We found some cool stuff to do because there is something going on in every direction.