I do plan to go to a Red Sox game
Good thing you're going in July - they'll probably win. If it were September, you'd be in for a laugher.
But seriously - lots of good breweries in the area. Sam Adams and Harpoon both have good tap rooms if you're into more of the mass produced stuff; Trillium, Night Shift, and Mystic are all great if you're into craft brews.
If you're into the whole witch stuff (though out of season in July), Salem could be a worthwhile trip (probably 45 mins from Brookline). An hour to Plymouth Plantation, but that's more geared to a crowd with kids I think. The Basketball Hall of Fame is in Springfield, but that's like an hour and a half from Brookline - plus other than the HOF, there's not much else to do in Springfield other than get shot.
A whale watch would be a good one (but pricey). The aquarium runs them, and the aquarium itself is pretty good. A cheaper option would be to just take one of the several harbor "cruises" that take you on a couple hour trip around the harbor and gives you a different perspective on the city. Museum of Science is again geared to a "with kids crowd". The rest of the museums are good, but pricey, (Museum of Fine Arts, Institute of Contemporary Art, Isabella Stewart Gardner Museum). There'll be some good plays being put on in the theater district if that's your thing.
Definitely check out Faneuil Hall. The Freedom Trail and Paul Revere's House are good for the history buffs, as is a tour of the USS Constitution in Charlestown. If you want to go bankrupt, let the ladies of the group take a stroll down Newbury street, which is like the Fifth Ave of Boston.
The Duck Boats are somewhat geared towards younger kids, but I'd still recommend doing them if you haven't done them before. The Swan Boats are good as well and a little more low key.
In terms of food, I think going out in the North End is a no brainer (authentic Italian), several good places to go there. Stop by Mike's Pastry in the North End for dessert (long line, but people rave about it). I'm not a cannoli guy, but if you are that's the spot for you. Otherwise, seafood. Legal Harborside in the Seaport is really good, but pricey. The Barking Crab in the Waterfront is cheaper and also good. Top of the Hub is a restaurant at the top of the Prudential Center - and it rotates 360 degrees, in like a half hour or something. So you get a birds eye view of the whole city from the second tallest building - can be pricey but not if you go for lunch.
Tom Brady's house is in Brookline - see if you can find which one it is so you can peep on Giselle.
Do Not, I repeat, DO NOT take the Green Line MBTA (the T) from Brookline into the city. The rest of the T is pretty good, but the Green Line absolutely blows in terms of time spent (because it goes above ground and has to deal with traffic, whereas the other lines are all below ground or don't have to cross streets while above ground), you can literally walk faster. Taking it to Fenway from Brookline wouldn't be the worst in the world though, since Fenway is on the southwest part of the city (nearest Brookline). Even if there isn't a game going on while you're in town - a tour of the park and a trip down Landsdowne street is cool (be sure to comment on Yawkey Way now being Jersey Street to really get some hot debates going with the locals).