Well, neither Shinjuku nor Roppongi are especially clean and the latter is not always safe but both can be fun at times. For all three aspects, maybe Shibuya fits the bill.
Originally Posted by keisari
I will probably be echoing what has already been said.
Have been to Tokyo twice (with different groups) and went both times to Nikko and did the day tour of Tokyo. Spent all 5 days in Tokyo.
Next time I am going to Kyoto.
The bottom line, if only 4 full days in Tokyo, skip Kyoto, do Nikko (nice get-away from crazy Tokyo) and enjoy Tokyo. go out at night around Shinjuku and Roppongi, its clean, safe and fun.
There is always next time.