Tokyo Metropolitan Government Building Observatories
Located about 30-minutes on foot from UNPLAN Shinjuku. The observation deck provides you good panoramic views of Tokyo and beyond. You can go up for free and there is a tourist information center on 1st floor, so definitely try and check it out!
*Reason for recommendation
This spot is well known because it not only offers an amazing view of the city, but it is completely free of charge to go up. When the weather is nice the view is truly something amazing and definitely worth checking out when you're in the area.