None of the flights were heading TO Boston.
Each flight has an origination point. Flight 93 while it may have been routed from Boston to the west coast that day, it could have very well have originated in NY. So in a sense yes Flight 93 FLEW TO Boston as Marky Mark pointed out.
There are connecting flights all over the country. Flying from New York to Boston then to West coast would have been considered a connecting flight in Boston. So yes the flight could have flown from NY to Boston like Marky Mark originally claimed.
For example I get on a flight numbered 1309 originating out of Chicago with a destination of Orlando Florida in mind. On our way we have a stop in Detroit. People get on flight 1309 in Detroit then fly from Detroit to Orlando. So you can see the flight headed TO Detroit then to Orlando. It quite possible could be the same way and the fact that Marky Mark had a ticket with the flight no. 93 TO Boston then bound for the West Coast.
Just because a flight comes from a city does not mean that it did not come a different city in the first place.
Not defending Marky Mark, but some people may be ignorant about how planes travel to multiple cities on a route.