I am a bit partial (since I own LTO) but in our hood (east village, manhattan) you can hit four more different record stores. there's Turntable Lab (lots of new stuff, great hip hop selection and have some cool store exclusives, no used tho.), there's us (down the street from ttl)... then Academy 12th street (it's a good shop that have some cool used stuff but sometimes it'll be hit or miss to find something you're looking for..), Stranded Records (which used to be Good Records but changed owners).. they're good for like soul, hip hop, world and some other rock but not a ton of used contemporary. and then there's A1, this is definitely a great place to find a real gem however, they don't really take care of their stock and you're definitely going to have to get on your hands and knees to find some good stuff. (I bought a misfits record from them for my collection like five years ago, it cost me 80 dols and it was on the wall without a sleeve on it..). and it sounds like you know about us.. so thanks for that.
Brooklyn has some great spots.. but one place I didn't see mentioned recently was Material World (used to be Heaven St.).. they have some awesome punk / metal and underground stuff,. Also Brooklyn Record Exchange is new and is co owned by some people who used to run CoOp 87 back in the day. (he was also in the screamo band Funeral Diner)... however I don't see them getting lots of newer contemporary used in either.. but to go there once and awhile, you're bound to find some awesome shit for cheap.
hope that helps.
kristian / limited to one.