In the United States we would almost never use either of these phrases. I'm sorry to sound evasive, but the fact of the matter is that in real life we know whether two places are in the same city or not. If I say "I'll take the bus from the Ruggles train station to BIDMC hospital," every knows this is an intercity bus and in their mind they picture a bus from the "T" system in their heads. If I say "I'll take the bus to New York," everyone knows that New York is a different city from Boston and imagines a big Greyhound bus.
Bus companies like to call their big, relatively comfortable busses "motor coaches" (or "luxury motor coaches!"), but everyone else just calls them "busses."
Examples of use:
"Take the 34E bus to Forest Hills."
"You can get almost everywhere in the Boston area via city busses."
"The bus to New York is a lot cheaper than the train."