I've recently added a list to my website that has links to book sellers that aren't Amazon or other large conglomerates, and I thought it might be appreciated here. This includes both eBooks (most DRM-free), and physical ones as well.
I found most of these by coming across books I wanted (usually via the fediverse or LibraryThing), and searching up the author's website. Usually they'll have the ubiquitous Amazon & Kobo links, but sometimes they also link to the publisher directly, who often have their own shops as well. Basically I do a lot of link hopping until I come across small indie places that are much nicer to buy from.
If you have any favorites that I haven't included here, please let me know! I'd love to add more.
UPDATE: Thank you all for the additional recommendations! I've added them to the page along with summaries of what they offer.
Powell’s Books
They’ve been big since before amazon got started and have survived and thrived as an independent company since. It’s the darling of Portland and it shows, every time I’ve been there it’s just packed with people, but I usually buy from their website.