Depends on the era and if we're talking about the overall fanbase or the Internet fanbase.
I'd say in the Switch/Switch 2 era Zelda has the lead. While in the N64 era it was effectively tied. In the NES, GB, and SNES era Mario had the lead. While in the Wii and DS era it was decisively Super Mario.
I'd say the Internet fanbase was overwhelmingly pro-Zelda until sometime between Celda and Super Mario Galaxy; Celda was controversial, I'd estimate somewhere between 30 and 50% were off-put by the new direction, and the game ended up selling significantly less, and driving less hardware than its predecessor. On the Gamecube, while it wasn't a popular game among the general consumers, online fandom was overwhelmingly favouriting Metroid Prime. Metroid quickly lost steam, and it was a shadow of itself by the time of Prime 3, despite a loyal contingent of fans. Twilight Princess looked like it would restore Zelda's position, but Super Mario Galaxy eclipsed it. Super Mario Galaxy was basically the result of the Super Mario 64-2 prototype, and it very much wowed the online fandom. For about a decade, Mario was prominent among Internet fandoms, and then Zelda won it back sometime between Mario 3D World/Land and Breath of the Wild. Many considered the old school linear "travel to the flag" type structure as being outdated and not serious enough. And Zelda has sort of reigned ever since.
In short:
It ebbs and flows no matter what strata of the Nintendo fandom you look at.
Generally, and amongst most Nintendo consumers, Mario is historically bigger.
Among online fandom it has usually been Zelda.
Currently: it's Zelda on both fronts.
I describe myself as a little dose of toxic masculinity.
