During the pandemic I got more into indie games and wanted to support small businesses and independent artists and publishers. I'll be adding to this list as I find more stockists.
UK
Mighty Lancer Games - My LGS stocks indie wargames (Osprey etc.) and is stocking more indie TTRPGs. Also has a huge stock of Reaper minis, if they count as "indie" and "print". This is an affiliate link, all store credit earned goes back into the hobby, but if you don't want to support the blog you can use this one.
SoulMuppet - Publishers of Best Left Buried and others (including The Stygian Library) and worth following their newsletter because of the other interesting projects they are involved in.
Iglootree - Independent bookshop stocking a range of indie RPGs as well as other non-mainstream books.
Melsonian Arts Council - Publishers of Troika! amongst others, and stockists of other TTRPGs.
Rook's Press - Independent stockist of a wide range of RPG zines.
US
Exalted Funeral - Stockists of many indie RPG materials.
LF OSR - Independent stockist and producer of OSR materials (including a print version of Knave).
International
DriveThruRPG (Print on demand) - Good selection and, based on my own experience of their UK POD partner, decent quality prints. This is an affiliate link and any credit goes toward buying books, but if you don't want to support the blog you can use this one.
Lulu (Print on demand) - Not one I regularly use but until recently the only source for Whitehack or Yoon Suin in print.
Non Print
itch.io - It would be bad not to mention that most of these resources I have come across linked from the creators' pages on itch.