You can, but you shouldn’t. Those comic bookstores will not offer you the best possible price for your comics, and if you’re parting with a rare, valued collection, you shouldn’t accept anything less. The alternative is setting up your own booth, but that could be costly and time consuming.
I think going online is the best way to sell your comics, as you reach wider audiences without too much effort or expense. But if you go down this route, please avoid eBay. Selling on eBay can be time consuming, especially if it’s your first time. You’ll have to create an account, write product description, take a lot of photos, answer lots of queries, deal with product returns, etc. And after that hard work, eBay will take away 10% from your profit, and then Paypal will take another 3% once you withdraw the money.
The best way is to go to a site like QualityComix.com who will pay you for what your comics is worth. Check out this link to see their comic price guide.