Well, depends on what kind of jeans you want - prices are pretty fixed on things like that, so it doesn't matter if you buy them at a specialist's shop, a boutique, at a department store, and it doesn't matter which city you buy them in either.
The depth of the selection at department stores wouldn't be as good as the standalone shops (though they can order stuff in, as the stores are not really part of the department store, they're just small store in stores representing their own brands), but check the department stores out - Isetan in Shinjuku 3-chome is like shopping heaven. Virtually every brand ever discussed on styleforum is basically carried under the same roof, and the food hall is pretty amazing too. The import stuff is all taxed here a bit, especially shoes, but the domestic stuff is interesting too. You could spend a day without getting out of the basement of Isetan, it's got a food hall next to a men's shoes hall - goes from left to right in price, from like $200 to $2000. Somewhere in the middle it gets good, the Tricker's are next to Aldens, next to the Crockett and Jones, next to the Alfred Sargents, next to the Carminas, and so on. Upstairs the 'young casual' floor has the Visvim is next to the Junya Watanabe, next to the White Mountaineering, next to the N. Hoolywood, next to the Julius, next to the Undercover, next to the Rick Owens, etc, etc. The MC-type stuff is on the next floor. Pretty spectacular sight for shoppers. Would be incredibly easy to drop five figures in there.
Shopping in Harajuku or Aoyama can happen, but you need a directory or map of sorts, and then be ready to cover a lot of pavement. Doing those places for real shopping is a good day in itself. If you are limited on time you can probably limit yourself to daytime walking between the area bounded by Shibuya station, up to to Harajuku station, then down Omotesando and then back right down Aoyama-dori back to Shibuya, plus the block down in Minami-Aoyama with the Prada store (must be seen) and then CDG and 10 Corso Como and Undercover in the back street. There's not that much daytime stuff to see at Aoyama itchome or Gaienmae, or up in Akasaka. At Gaienmae there's Aoyama Bell Commons - you might want to check out Cibone, it's a pretty cool design shop with a mix of imported stuff and Japanese stuff.
What are you gonna eat in Tokyo?
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