Trade Authority (it's in The Well, which you can access from the elevator to your left when you enter the train station at MAST; if you haven't done any quests that take you here, you may not even know there like an entire second city underground)
All I can remember the names of; there's another gun store somewhere in the residential area that doesn't look like it would even be a store, and probably something I am forgetting about down in the Well.
Honestly, I don't like New Atlantis because the shops are so spread around and it has the oddest city layout I've ever seen. I get so lost here all the damn time, I prefer to shop in Neon. Everything important is on one strip, which the fast travel marker takes you right to the center of.
Centurion Arsenal in the residential district sells ammo, but shit is kinda expensive. wanted to buy some 6.5 for a well modified maelstrom and it was like 1000 credits for 60 rounds which is kinda high for me early game so id rather just pick it up.