{Large, country} syntax used by CityData has a fixed threashold of 100,000 people. Also, notice that
CountryData["USA", "LargestCities"]
is fixed at the top 100 cities by population.
To use your own population threshold, apply a filter to the list of fully quilified city names. Then use that new list for pulling up all the other properties. This particular approch is not the only way and it is not paritcularly fancy, but it does the job in stages, so we can see what is going on.
usCities = CityData[{All, "UnitedStates"}];
allUSPop = CityData[#, "Population"] & /@ usCities;
togehter = Transpose@{usCities, allUSPop};
threshold = 200000;
filterPop = Select[togehter, (#[[2]] >= threshold &)];
filterUSCities = filterPop[[All, 1]];
Either of these approches can be combined with the "Alaska" | "Hawaii" exclusion list given by Brett, directly in your existing code,
DeleteCases[CountryData["USA", "LargestCities"], {_, "Alaska" | "Hawaii", _}]
DeleteCases[filterUSCities, {_, "Alaska" | "Hawaii", _}]
