My theory on this is
buy from where you'd like to be able to shop in the future.
For instance, if you like having a local independent bookstore, buy your books there - that way, you're helping to ensure that they stay in business.
You can also check out Indiebound to help you find independent bookstores!
There are of course still some chain bookstores like Barnes and Nobel and Borders - again, buy your books where you want to keep being able to shop for them.
If you want to order a book on-line, check out Powells (a large independent bookstore that I really like, and that I've chosen to team up with here on this website - when you click a book cover on a book post at this blog, it usually takes you to the Powells page for that book. (Full disclosure: I'm part of an 'partners program' with Powells, which gives me a commission for business I send their way.)
Of course, there are other, larger online stores as well - Amazon is a giant, and often works with Affiliates to offer them commission on any click-throughs. So, if you're shopping Amazon, go to them through blogs or websites or organizations you'd like to support.
And if you can't afford to buy all the books you'd like to, contact your local library - either get the book there (the more GLBTQ Teen books circulate, the more librarians will see the books are in demand and the more GLBTQ Teen books they'll buy for their collections), or if they don't have the book, see if you can request they either purchase it for their collection or get it for you through the inter-library loan system. (I've gotten books from clear across the country this way!)
Thanks for asking, and happy reading!