All those shops you're referring to are in Ochanomizu, which is right next to Akihabara.
If you're staying in Shinjuku there's no need to go any further than Shinjuku, Shibuya and Ikebukuro, all of which are on the Saikyo train line, which is much faster than the Yamanote since it doesn't stop at all the stations you don't need.
If you're much of a walker you can actually walk to all three locations by staying on the Meiji Dori, one of the major arterials on the west side of the Tokyo metropolis.
I never keep track of the names of a lot of the stores I go to but in Ikebukuro there are 4 major stores, 4 in Shibuya and 3 in Shinjuku.
Ikebe, Ishibashi, Kurosawa and Key are some of my favorites.
There's live music every night with no cover charge at What The Dickens, which is about a 5 minute walk from Ebisu station, the next stop after Shibuya.
If you do decide you want to fight the crowds in Ochanomizu then you'll want to catch the orange marked Chuo line from Shinjuku and not the yellow one which stops at 8 stations by the time you arrive, instead of 3.