The observation deck in Bunkyo Civic Center is very nice. It is on the 25th floor, free, good for a 270 degree view and the windows are obliquely placed so you can look down relatively well.
The sun goes down behind the sky scrapers in Shinjuku and you have a beautiful view of Sky Tree.
I see you wrote Korakuen between parentheses, so I think you mean Koishikawa Korakuen, the garden near the Bunkyo Civic Center. It's a typical Japanese garden, quite large and beautiful, although it will be too soon for autumn leaves and the entrance is not free (200 or 300 yen). But I think on October 1st the entrance might be free. Rikugien garden is a little bit further but is more beautiful in my opinion.