Many cities have been cited as being attacked, only New York, Columbus, and Cheyenne have been explicitly named as surviving the attacks. The numbers and specific cities have varied between episodes, this may be because the writers didn't want to tie themselves down or because they intended it to reflect the panic and confusion such a large scale attack would induce.
What follows is a rough list of those cities that have been at various times mentioned as possibly being attacked.
Albany NY, Atlanta GA, Baltimore MD, Boston MA, Charlotte NC, Chicago IL, Cincinnati OH, Dallas TX, Denver CO, Detroit MI, Hartford CT, Houston TX, Indianapolis IN, Kansas City KS, Las Vegas NV, Lawrence KS, Los Angeles CA, Miami FL, Minneapolis MN, New Orleans LA, Norfolk VA, Philadelphia PA, Phoenix AZ, Pittsburgh PA, San Diego CA, San Francisco CA, Seattle WA, St. George UT, St. Louis MO, St. Paul MN, Washington, D.C.
The season premiere of season 2 announced that 23 cities were attacked.