Nidoqueen is almost a perfect counter to Togekiss. Rotom-H is niche, but is another full counter. Raikou and Rhyperior are very solid checks. There are a bunch of other potential checks depending on what set it's running -- Fletchinder, Doublade, Mega-Aggron, Gligar, Mega-Aero, Crobat, Jirachi...