To be honest, the clam shops along the beach usually have better chowder than restaurants but she'll probably just be hanging around town sooo...
The following are all right down the street from each other.
Jimmy's Harborside - 242 Northern Avenue, past the World Trade Center (across from the No Name previously mentioned at 15 1/2 The Fish Pier) - either restaurant is good.
http://www.jimmysharborside.com/
Barking Crab - Northern Ave Bridge/Sleeper street - great on a warm day, casual, boaters tie up and tie one on. A summertime favorite of mine.
Anthony's Pier 4 - 140 Northern Ave. - one of the only restaurants in Boston where you can actually dine outside, waterfront. A bit of a dinosaur, but an institution, and the food has always been good when I've gone there.
http://www.pier4.com/
Normally any pub or local restaurant she goes into is going to have it and it's going to be pretty good.
Make her promise to stay out of Legal Seafoods and the Union Oyster House. There food isn't awful, but there clam chowder is potato chowder with the possibility, but not guarantee, of some bivalve in it.