Between Boston and the Cape?
I'm flying into BOS around 9pm on Thursday night before driving up to the Cape (Wellfleet to be specific).
Is there anywhere inspired to stop on the way to eat other than the highway choices?
What kind of food are you looking for?
When we stop en route to the Cape, we stop at Wood's in Plymouth for Lobster Rolls (right on the pier, next to Lobster Hut and CabbyShack).
There's lots of Cape Cod suggestions on the Southern New England board here, too.
25 Town Wharf, Plymouth, MA 02360
Normally, I'd reccommend the Tuscany Tavern on Rte. 3A, north of Plymouth Center. Great Italian food prepared by two women in a small open kitchen. But be warned, if you are arriving at 9 pm, no restaurants will be open by the time you get out of baggage claim at Logan. They are the slowest, it will be 9:45 (at least) before your bags get to you. Plus, you have 2 more hours to Wellfleet.
294 Court St, Plymouth, MA 02360
Since you may not be out of Logan much before 9:30 or 10, I'd say maybe hit Victoria's Diner, which is just off the Expressway (Mass. Ave. exit) immediately south of downtown Boston. They are open all night long on Thursdays, and the food is generally very good.
Boston, MA, Boston, MA
kevinricci is correct, Logan baggage handling is ridiculously slow. As are Logan car rentals. You will be lucky to be on your way before 11, so an all-night diner may be exactly what is required. Or Chinatown - New Jumbo Seafood is open late.
Jumbo Seafood Restaurant
7 Hudson St, Boston, MA 02111