As an American, you should pretty much automatically get a 10-year multiple-entry visa that permits a stay up to six months per entry if you apply at a consulate/embassy in the U.S. It runs about US$150. Yes, that's more than a single electronic visa, but it's nice to have for any future trips, and you won't have to worry about problems if something happens and you have to stay longer than 30 days in India. (It's still good even after your original passport expires.)
Kochi is still nice, but Kovalam is not particularly anymore. Varkala still has a very relaxed atmosphere and a great setting on a cliff overlooking the sea. But it's not a particularly upscale sort of place, if that's what you had in mind.
Compared with major Indian hilltowns like Darjeeling and Mt. Abu, Munnar is a tremendous disappointment.
The backwaters are very beautiful.