Honda has a far better track record for reliability. However Yamaha seems to be favored as a track bike.
They both make very precisely engineered machines, so you shouldn't have any hesitation about buying a bike from either company.
Just a note..there's been more than a few confirmed cases of Honda bikes making it over 100k miles with nary an issue. That does include the CBR range of bikes along with the goldwings and some of the cruisers..