Air has different risks, I wouldn't assume it's safer. Given the accident in Spain, I assume it's far more dangerous. That accident left a 2km^2 mess of plutonium.
There are specially-equipped subfleets of C-17s and C-130s available to the Nuclear Airlift Force but that's all I know. Some of the former were used last year to remove HEU from a facility in Scotland.
In the olden days the USAF used to cart weapons around by the dozen, literally, in C-124 transports nicknamed 'Old Shakey', which shows how resilient these devices are.
During the Cold War the Soviet forces used An-22s and Mi-6s for similar missions. The latter would have deployed weapons to the GRU handlers at air-bases immediately prior to use.
Nuclear weapons are big. And according to the article, the weapons and parts thereof are being trucked all over the country constantly. Presumably sending them by air would be prohibitively expensive.
