I second Dormy Inn, I have stayed at Dormy Inn and pleasantly surprised by the quality for the price paid. Sure it is no Five Start hotel, but for the price I was pleasantly surprised of the quality. Dormy Inn Shibuya-Jinnguu is located pretty much midpoint between Shibuya station and Harajuku station. Compare with other hotels you listed, walk from the train station to Dormy Inn is little further. One note about Dormy Inn at Shibuya-Jinnguu location, many Dormy Inn locations have all you can eat breakfast if you choose breakfast option. However, Dormy Inn at Shibuya-Jinnguu main portion of breakfast is not all you can eat. Soup, salad, and fruits are all you can eat but anything else is not all you can eat at Shibuya-Jinnguu location.

I would not get hang up too much with Shibuya vs. Shinjuku. Both are very close to each other, less than 10 minutes ride on JR or subway. Access to Roppongi is in terms of journey time from either Shibuya or Shinjuku is pretty much same. Using New York City reference, it is like deciding to stay near Grand Central Station or Penn Station. Many will say that both are close to each other by quick subway ride, and not to hang up too much about area around Grand Central Station vs. Penn Station.

In general I think Shibuya and Shinjuku both have pretty much everything. You can be specific and say one has this but other do not. However, general stereotype among Japanese is that Shibuya is more for younger generation than Shinjuku. I do not have idea about today’s club/disco scene at Tokyo so I cannot say. But as for restaurants, both Shibuya and Shinjuku has plenty.

I think it is difficult to use downtown/midtown/uptown concept of New York City into referencing Tokyo.