You could check out Portsmouth, NH. Strawberry Banke is a really cool way to spend a couple hours while there. We also did a lighthouse tour that was awesome. Portsmouth is about an hour north of Boston.

who will be in the group? and what sort of things do they like?

Plymouth is close and has a few things to see. in addition to the plantation, mayflower replica (if it is still there), and beach if you want to go there are things like graveyards with some of the mayflower passengers buried.

Salem is just north of boston and has it's tourist stuff but is an interesting little town. Can do sailboat trips, visit nathaniel hawthorne's house, loads of old graveyards and historical and ghost walks.

i haven't been on the cape for about 20 years but we used to go for the whale watching trips from Provincetown (you could also go from Plymouth, Gloucester, or loads of other places in the area but i think P'town is the closest). We must have been from various places up there well over 10 times and have always seen loads of whales.

Another option north of the city is Marblehead (right next to Salem). Plenty of history and the Old Town section is great for walking around and poking into shops/restaurants. Some incredible seaside views both at Fort Sewall (Revolutionary-era fort perched high on a bluff overlooking the harbor) and out on Marblehead Neck.

Another option if you like history is Minuteman NHP, checking out the battlefields at Lexington Green and the Old North Bridge in Concord.

Sox are away that week but Fenway is open for tours, definitely worth it.

As far as the Cape, I'm partial to Falmouth/Woods Hole area (great running/biking options). Since you are there just after Labor Day, will be less hectic than it is during the summer. Only about an hour or so from the city so not too far out of the way either.

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"You can never win or lose if you don't run the race." - Richard Butler

I grew up near Boston and we always went to the beaches in Newport Rhode Island. I always loved that area.

You also could head inland based on your interests- the berkshires have great hiking. If you’re a history buff the Concord area where the revolutionary war started is pretty interesting.

Just my wife and I. SOS is the next weekend so while we are active keeping it low key. Really like the historical aspects/ tours especially as we’ve not been to that part of the country.

We live in Los Angeles. Have to drive 2 hours just to be out of the city (a little hyperbole). 4 hour drive we’re still in California. So the options seem overwhelming here LOL

Lots of good suggestions here. If you're up North Shore around Marblehead/Gloucester, you can also wander through a bunch of antique-y type stores that line Rte 133 through Essex and Ipswich. The lobster rolls at Woodman's in Essex are pretty good. Crane Beach is close to there as well.

If going down the Cape, I agree with Brian in MA, Falmouth and Woods Hole area is nice. Chatham isn't bad either - I generally like the ocean side of the Cape more than the Bay side. If in Falmouth/Woods Hole, consider visiting the Woods Hole Oceanographic Institute.

Lowell has some really interesting museums on the industrial revolution.
Harvard's museums are very nice
Lexington & Concord
Newport RI is about 90 minutes without traffic
New Bedford has interesting whaling museums
Fall River has Lizzy Borden's house, in a scary part of town
Nashua, NH has a lot of tax-free shopping
Wrentham, MA has an outlet mall. Mass doesn't have sales tax on clothing below $175 (and then only the part over $175 is taxable)
Mt Wachusett is between Worcester and Fitchburg and on a good day has a nice view of Boston
Monadnock is between Nashua and Keene, NH and a nice mountain to hike up in about 60 minutes. About 90 minutes out of Logan without traffic.

However, if there are any hurricanes coming by, avoid Scituate and Plumb Island, and the whole cape.

Drive to Providence, jump on ferry to Newport, 50 min only 10.00 through Narragansett Sound.
Best way to see north shore of Boston is, if you can, rent sea kayaks.
Evening in Boston area, take the T (subway) to Harvard square, walk around Harvard Yard, go to Club Passim, historically old "coffee" house

Suggestion: get on the ferry from Boston to Provincetown. Could probably uber out to the Cape Cod National Seashore. Outer cape is nice, Hyannis is an armpit.

Anywhere you go, good luck lodging and possibly traffic

One thing to be careful of- protect yourselves from ticks. So many people I know on the cape have Lyme. That would not be a fun souvenir to bring home.

i am sure there will be a hop on hp off buss tour company in boston - probably several. Always a great way to get informed while getting round the interesting places in the city.
.......i first went to Boston shortly after arriving in the US on a work visa. i had heard of the Boston Tea Party so wasn't completely unaware of american history .....but thought Sam Adams must be a famous beer maker.......

the thing i remember most from the tour is seeing the Cheers bar from the outside.

i am sure those that live there can give better recommendations on where to run (if you are training at all) but when I've been in the city on business there seemed to be lots of fit people running along the Charles River

marathon finish line and adidas run base - they have linden's jacket, super cool

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maybe she's born with it, maybe it's chlorine
If you're injured and need some sympathy, PM me and I'm very happy to write back.
disclaimer: PhD not MD

Actually - labor day - spend some oogling time on the Charles river greenway = coeds will be back in town