Your LGS is in a retail space, paying retail rental prices, providing retail amenities. They will be subject to every tax your country, region and city levies.
Amazon's locations are largely in light industrial spaces, paying lower rental prices and have no concerns about catering to physical customers. They will be taxed at a different- usually lower- rate than your LGS. In addition, they have economies of scale and the ability to cross-subsidize or manipulate prices in many ways your LGS cannot...often for extended periods of time.
Each company's markup will be due to a mix of good & bad business decisions and projections & perceptions of what is needed to maintain profitability. Amazon has a LOT more room for error.
These things add up.
You have to decide whether the personal services your LGS offers are worth paying extra for, because if it isn't, that LGS will ultimately fold. Think of it not just as paying for Product X, but as an investment in having that place around in the future.*
It may be that your LGS is not worth supporting. Service may be shoddy, for instance. Or their markup may be pricing products out of line, not only with Amazon, but also with other game stores in the area.
But again, that's calculus only you can do.
* a doctrine called "enlightened self-interest".