That's a tough choice, but I gotta go with Frankenstein. Gargantuas is my personal favorite, and I think the story idea is superior; the whole brothers-at-odds thing is classic, and Sanda and Gaira seem like a perfect match-up over the completely random Frankenstein vs. "Giant Monster Who Came out of Nowhere."
Still, Frankenstein is somehow more entertaining. Frankie definitely evokes more sympathy than Sanda, and Nick Adams surely puts in a better performance than Russ Tamblyn (not because Tamblyn's a bad actor; Adams simply relates to the Japanese cast better. Russ is lost in Gargantuas). And then, of course, there's Baragon. While random (don't giant monsters just pop up in Japan all the time anyway?), he undoubtedly earns his reputation as a fan-favorite.
Plus, Frankenstein has so many great moments: Frankie throwing the television out of the window, Baragon crashing a resort party, and so forth. Classic. I'm just sad I didn't see this until Media Blasters released it. This movie would have grown many wonderful nostalgic memories. Instead, I had sweat-slicked nightmares about furry green man-eaters!