The ones that I know of are:
Fame (address: Nieuwezijds Voorburgwal 182) wich is inside a small kind of mall. They used to have a huge store but they had to move to a smaller one due of declining recordsales. They used to be quite good, don't know what they're like now.
Independent Outlet (address: Vijzelstraat 77). They call themself Amsterdamís most hardcore skateboard, punk, clothing & shoe store since 1995.They used to have a basement packed with vinyl and cd's. Last time I went there they changed the place and the basement was gone. They still got some vinyl left though.
And these are some I found on google. Haven't been there so can't you tell anything about them.
VelvetMusic (address: Rozengracht 40). They've got a small store at the Lowlands Festival which was alright. The pictures on the website look nice though.
Distortion Records (address: Westerstraat 244). I've never been there. Don't know anything about the store but their online catalogue seems allright.