I've bought comics at both types of stores. My current shop - which I've been going to for 6~ years or so - isn't really either one of those. The most important thing for me is a good staff/owner. Are they approachable? Can I have a conversation with them like a normal person? Are they knowledgable about more than just the books they personally like? Can they make good recommendations? Etc.

I love my current store and haven't stopped going, even though there's another store that is is actually much closer (3 blocks from me).