Breath of the Wild. I agree with the OP's reasoning. Pokemon will definitely (and probably has already) overtake BotW, but BotW will no doubt take it back in the end. And until you pointed it out, I didn't realize how close the sales numbers were for the two in Q1. Even with Pokemon's DLC and lack of a third version, BotW will outsell it within ~2-3 years and stay on top forever.
Also, let's not forget that we're only talking about the Switch version here! If we include the Wii U version (more than 1.5M but probably less than 2M) than Pokemon might never outsell BotW, even temporarily.