I've googled this a lot in Japanese, but with very few results to show for it.
In PCE magazines, they released sales rankings with "scores" that were based on the actual sales number divided by some mystery variable. To make matters worse, every now and then, they even changed the variable. If we could find out some hard numbers for particular games and make up a database of all the "scores", we might start to get somewhere, but there just isn't a reliable enough source out there.
A lot of people do say that Tengai Makyo II was the best selling game, but even then, the numbers are all over the place. There was a magazine that said 500k. Hudson said 300k. The writer/director said 200k. And there's a sales records website that says 130k.
I personally think there is room to doubt whether TMII really was the top selling game. We know from multiple reliable sources there were about 1 million Japanese Duo owners, about 3.8 million base PCE owners, and that about 1 million of those base PCE owners had the CD expansion. That's twice as many people who can play Hucards as can play CDs. Personally, I wouldn't be surprised if the best selling game is one of the Hucards from late 1989/early 1990, just because that was the peak time for the system.
This chart came from a PCE magazine from 1993 (I think). The bars are base PCE systems (white) and CD-ROM systems (black) and the lines are total Hucard sales (red) and CD game sales (green). The left y-axis corresponds to the systems, and goes up to 4 million, while the right y-axis corresponds to game sales and goes to 6 million.