lyn,
For last night stay, my view is depending on your flight back.
If early morning flight, stay in Narita hotel. It is easier the next day as time to airport is so much quicker. Transfer to Narita hotel at evening time the day before.
If late afternoon flight, stay in Shinjuku and move to Narita in noon.
How are you transferring from hotel to airport?
In Shinjuku, the big departmental stores close at 8pm. If you want to do shopping, do plan to do so at earlier timing.
For restaurants, there are lots of them in the Shinjuku area, along main road & in small alleys, in some office buildings. Depending on your group size, try to get a bigger restaurant for seating. Quite a number are small in capacity.
Can try restaurants at departmental stores higher levels, some are bigger in comparison, more spacious though more ex.
We had occassional showers when we were there - do bring umbrellas and/or rain jackets. Or check Japan weather forecast before you leave SIN.
Have fun and enjoy your trip