Great time to come. Boston is "empty" what with all the college students gone for the summer (like 100,000 less SUVs clogging the streets).
Boston is, however, a complete mess for road construction right now, so drive carefully and plan ahead. I'm not kidding, downtown it is often impossible to get from point a to b.
Charles Street near Beacon Hill: Many nice little shops, often expensive though.
Newbury street: Ultra-high end at one end, getting progressively trashier/affordable at the other - something for everyone and many cafe-seating restaurants.
Copley area: Several indoor malls and interesting places in general like Trinity Church and the Hancock tower (the moneyshot for tourists).
Boston Public Garden is nice. Not to be confused with the Boston Commons which is less so.
Cool thing is that all of the above are doable in a day and all near each other.
I won't say one place or another but take your pick, fantastic dining can be had on/off Hanover St.
For the worst service anywhere, with authentic totally Bostonian asshole attitude, go straight to Pizzeria Regina. Marvel at how the pitcher that serves four actually costs more than four individual drinks - plus you need to do the work of pouring. Go figure.
Canolies at Mike's Pastries. Do it.
Drive and park there only if you are a "made man", terminal, or stupid. Use the large parking lots nearby instead of the street.
The ill-named "Tsunami" restaurant in Brookline near Coolidge Corner is simply the best sushi I've ever had in America. Go before the name alone puts them out of business.
The Druid Pub in Cambridge is THE best (i.e proper) Guinness, although hope you don't go on trivia night (why my Irish brethren like that crap is beyond me).
And ideally will have just visited Punjabi Dhabi a few stores down for the most authentic Indian food anywhere (not a fancy restaurant at all, everything is on cafeteria trays and you won't care! It's packed usually but just go upstairs.) Makes my Indian friend say: "Jesus Christ this is so good!". Your clothes will reek of spices after, though. Both in Inman Square.
The Faneuil Hall area is the tourist trap. Okay I suppose, I never go there though. There is an aquarium nearby. Museum of Science near Cambridge is ok too. Don't forget the MFA Museum of Fine Arts and Gardner museum. And the old wing of the Boston Public Library is worth a peek.
Bunker Hill monument has sadly been eclipsed by the idiotic and competitive pyramid caps of the nearby Zakim bridge, which says "Nyah, nyah, you're just a filthy old obelisk, we're a shiny hard-working bridge". Anyway go inside the monument for a chilling reminder of the Masonic cult that runs this world. (A huge masonic symbol statute is at its center.)
Arnold Arboretum is a nice place to fly a kite or just chill, with a great view of the Boston skyline.
And the Boston side of the Charles can be quite lovely at times. (Sad that it is also the point of two major roads though). You'll need to go over to the skinnier/noisier/less shaded Cambridge bank to get nice pics of Boston though.
And Chinatown (not big at all) has some cool shops and good food tucked away but that's more trial and error. "Pho Pasteur" is an excellent Vietnamese chain around Boston for those big ass bowls of soup. Delicious.
The Porter Exchange mall at Porter Square Cambridge is packed with Asian/mostly Japanese restaurants. Convenient to Harvard if you visit there.