Closest ones to CTF that I know of.
http://www.stmarkscomics.com/
This is a small store but for whatever reason they always hire a cute girl for the bag checks LOL! They carry SF and have an insane amount of old school toys in the back. You can take the 6 train to Astor Place and walk the difference.
http://www.fpnyc.com/
This is a BIG store, it’s within walking distance of CTF, just go up Broadway until you hit 13th Street, or just hope on the 6 at Canal and get off on 14 Street Union Square.
There’s a REALLY small one that’s super close to CTF, it’s after Canal, I THIIIINK on Elizabeth St., but it’s really small… Don’t know if they carry SF though.
The next closest to CTF is Chameleon comics. SRK poster Fact4Life works there. You would have to take the J train downtown and get off at Broadway Nassau. It’s a small store but they have a great collection of TPBs.
http://www.superpages.com/bp/New-York-NY/Chameleon-Comics-L2012020280.htm
Another big store, across the street from the Empire State Building. There’s a Black guy named Larry who works there and is very cool who knows LOTS about comics. LOL anytime some comic book story hits the news he’s always getting interviewed. Good guy to talk to and stuff, ask him about the latest comic book movie for laughs. 
http://www.fpnyc.com/
The other biggest stores are run by Midtown Comics. They have two spots, one on 40th between 7th and 8th and another on 45th and Lexington. The one on 40th is better because they’ve been there longer and I’ve had lots of problems with the one on 45th getting their books on time, but SF’s always there. SRK poster Kourin-Chan used to work on the one on 40th.
http://www.midtowncomics.com/
Oh and there’s a Japanese bookstore nearby where you can pick up Arcadia Magazine, or sit there and flip through it for free LOL! We get Arcadia in NY like the first week of every month, so slower than the West Side and Japan - NY is a lot farther away ha ha!
http://maps.google.com/maps?hl=en&um=1&ie=UTF-8&cid=0,0,1196359249647498391&fb=1&split=1&gl=us&dq=asahiya+new+york&daddr=52+Vanderbilt+Ave,+New+York,+NY+10017&geocode=14468292608759845815,40.754994,-73.977792&sa=X&oi=local_result&resnum=1&ct=directions-to
OK I think you’re good. 