They are both really great, but I'd say Pinkerton. The b-sides and the never before released tracks are amazing and I listen to them a lot more than the Blue deluxe tracks. I also really liked the edited version of Pink Triangle. Not to mention the indepth liner notes about the creation of Pinkerton, and the letter from Rivers which explains his leg operation and hopes for the album which gave a much more personal feel than Todd Sulivan's notes on Blue.
Although I will agree there is a huge saturation of Pink Triangle and Good Life live tracks. But it's still great nonetheless.
Definitely Pinkerton deluxe. Way more material. I think that the Blue album should've had some accoustic stuff and radio sessions like Pinkerton, but even if not for that there's "Surf Wax America", "The World Has Turned and Left Me Here", "The Sister Song" and "Let's Sew Our Pants Together" demos that are all missing.