Overall, I preferred the antiques shop. It's not massively exciting in terms of ghost activity, but then it fits in with the rest of the game! (Ba-dum tsh)
But really. The design is so nice. It's big! It has nice rooms, about fifty million clocks, the entire entrance has lights on every spare inch of ceiling and cups all over the place, plus a banana cheese... something on the menu. It's lovely.
Rei's house is pleasant, and nice to be in, but it doesn't really have the overall "what in the hell is this place" atmosphere that I like so much about the crazy cluttered antiques shop and Hisoka's lovely room and everything. Yuuri's little sunflower calendar. All it's really missing is something like Miku's room... but Miku is still too raw so I'll leave that thought there.
Rei's house definitely trumped it for me in terms of hauntings. I much prefer the way they use the house and just kind of subtlely stick a ghost in your kitchen, or shower, etc. I like a couple of the things in the shop (primarily your dead friends showing up, and Tall Woman on the CCTV camera is one of the top 3 moments in the game), but it all comes too all-at-once and in your face.
Plus the shop has actual boxes of tea everywhere. That helps.