(williamsburg -- n6th st between wythe & berry) seems to be considered the best place in new york
there are a few other record shops in the area, e.g. soundfix
on berry st: have a wander around.
(greenpoint -- guernsey st) opened since i was last in nyc & looks to be worth a visit for sure, believe it's a captured tracks/ mexican summer venture so possibly the best bet for pop stuff.
manhattan (all relatively close)
(e 4th st between lafayette & broadway) is overrated but has to be done
st marks bookshop
(3rd avenue between 8th & 9th) isn't a record shop but it's near other music & a great shop
(thompson between w 3rd st & bleeker) is a good punk/hc shop, excellent basement
(1st avenue between e 7th & 8th) is pretty decent, pity their other branches shut down.
(ludlow st between stanton & rivington) has a few records. then go check out abc no rio
these are the decent ones i found. i'm sure there are glaring omissions, maybe someone who knows the city better can suggest some. new york is ace, can't wait to go back.