My wife and I were able to stay at the Hilton Tokyo for 5 nights and we enjoyed it. As said above, Shinjuku Station is the main station. From there you can go to other places. The list below is what we did during our stay.

• Robot Restaurant. Other have said it's kinda cheese but you have to visit once.
• Tokyo Tower
• Owl Cafe
• Tsukiji Market.
• Imperial Palce.

I would also recommend getting the Tokyo Metro Subway App. Easy to use. It seemed that we spent more time traveling between places than actually spending time at the destination.