Nippori is a good neighborhood for fabrics and is on the JR Yamanote line. Here is a map
http://nippori-senigai.com/free/map
And some directions with photos
http://blackcabbit.wordpress.com/201...tores-nippori/
(Ditto armagebedar!)
As far as I know, it isn't a united wholesale market neighborhood like Dongdaemun in Seoul where one can buy both finished garments and fabric in bulk.
Shinjuku also has Okadaya and Yuzawaya craft stores which carry fabric
http://blackcabbit.wordpress.com/201...ores-shinjuku/
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I don't have the knowledge to speak about Tokyo fashion but I do know there's quite a few subcultures which don't necessarily reside in the same shopping areas.
By underground Arts and Fashion, do you mean more independent styles often associated with youth culture sometimes generalized as Street Fashion like these?
http://tokyofashion.com/brands/
http://www.tokyofaces.com/
http://en.wikipedia.org/wiki/Japanese_street_fashion
If you have a specific fashion subculture you're interested in (as there are many tribes) then you might want to search in those types of forums for such neighborhood and shops.
Here's a slightly older rundown of some of the fashion subculture styles
http://wuggitywug.blogspot.com/2011/...on-styles.html
Fashion Maps
http://tokyofashion.com/fashion-map/
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What's your hotel budget and are you paying with points or cash/credit card?
If you're interested in things more in the Shinjuku, Shibuya, Harajuku areas then Shinjuku and Shibuya offer upscale and business hotels. Ikebukero or Nishi-Shinjuku might be a bit more affordable but you'll need to take the subway/JR to get to your destination. The Tokyu Stay chain has locations in Ikebukero and Nishi-Shinjuku which offer a business hotel like atmosphere + washer/dryer in room and usually a bit more space which is good if you have extra luggage. There's also the Dormy Inn Premium Shibuya which is between Shibuya and Harajuku.