Some of these questions, no one can answer but you depending on how much time you want in each place.

Re; opinions on JFK and Harvard Sq in same day -
when we bring visitors to Harvard Sq/ they spend hours - depending on day , weather and interests -
the museum, street performers, stores, walking around campus, depending on what is showing theater/comedy/etc and a meal -

you are coming in July, it could be hot, your hotel has a a pool, and you have teen boys -

so for me, going it the morning to, say, something close to your hotel, and possibly taking a swim/break around lunch and then heading say to Harvard Sq for from 2pm through dinner

and then doing JFK another day, again say after breakfast - and then seeing what the weather, day and other things on your list to do in the afternoon - maybe you'll take a break, maybe the boys will want a swim and do that afternoon and evening in the North End - doing the freedom trail things in that direction and staying through dinner -

This is why I think it is nice to lay out a general idea - we usually have a list of our must sees - our absolute can not go home with out seeing/doing - and our next in line - if we can fit in - and we do our best with the list without exhausting ourselves and allowing for some fun and breaks.

Maybe your boys will zip through the JFK museum and you will all want to continue on to Harvard Square -
I think it is best to have several choices and go with the weather (hot, rainy, etc)

I would do Duck Tour, first thing, first morning of arrival if weather permits - I would print out Freedom Trail and become familiar with neighborhoods and areas before deciding when and how to do it all -

I would tell the boys to google Boston, attractions, etc and get them to maybe choose some things -
a boat ride - of the many Harbor Islands - esp in summer is always a good choice -

If you go to Provincetown/MV or somewhere else or not, maybe the beach (while not the beauty of an Ipswich certainly) but if you would be satisfied with a boat ride, a hike where you get great views of the Boston Harbor and islands, swimming beach, bbq, etc - you could go to Spectacle Island for 1/2 a day - see if something on their schedule appeals to you while in town

www.bostonislands.org/isle_spectacle.asp

and I think it is fun to end with Pru Skywalk too, b/c it brings a lot of 'we were there, we saw that' etc.

As far as dining, personally, I have not been to Durgin Park in so long, since it long ago lost , for me, all the reasons growing up that is was so unique -

If the boys like a good burger, and sports, you might consider Clery's Irish grill on Dartmouth Street, not a far walk from your hotel - great burgers as well as other things and large screen tv's and family atmosphere before it turns to a young crowd at night -
I agree about Charlie's for a substantial breakfast that will hold you if you like diner type old fashioned good eats -
for dinner, Giacomo's also on Columbus is affordable and good italian if you want it again without going to the North End

Legal Seafood would be my first choice -

You could also consider the Parish Cafe on Boylston St for lunch or dinner, you can search and find their menu and prices online -

Someone also suggested chowhound, I think in a previous post, which is a good suggestion for you to find only food opinions.

I think the option to take a 'swim break' during the day will work well for us. Good to have all the suggestions for activities--and I also really liked the menu for the Parish House. It's a place I hadn't come across in my research.

Would you try to do the Freedom Trail on July 3 or 4 or would you do that earlier in the week before it gets even more crowded? Also, people have said to walk down Fairfield for a view of the fireworks. Is that close to the Sheraton and is there someone in the vicinity to eat?

Yes, you can walk to Fairfield
For eating: you will on your way be in the midst of a zillion restaurants ( crossing Newbury, Boylston, Copley Place, etc) also some good spots on Charles St, etc - look on opentable.com and you can choose to look by location , date and time and see what is open and look at some menus, even make your reservations online, which isn't a bad idea during a high season week.

To help you see how close things are, you should print out a street map of Boston - and ones that help you gauge walking times - it is a small, walkable city -

look at this map for example: here is a tiny url to a good Boston walking map -

http://tinyurl.com/4yjrxy

this is one of the many maps, but the one I think will most help you at first, available on

www.walkboston.org

when you go to Walk Boston - click on resources, and then on maps - they have many walking maps of the city and also interesting points - you can print out and bring with you if there are areas listed you would like to venture to -

Look at a map and see where Boston Common and Boston Garden are and how the street then is Arlington, Berkeley, Clarendon, Dartmouth, Exeter, Fairfield, Gloucester, etc, etc, - alphabets of sort and works its way down to Mass Ave - and these streets cross Commonwealth, Boylston, Newbury, etc -

learning this grid will give you an idea of that area - then you can look at waterfront area, etc -
google maps

Good to buy a Fodors/Frommers/ pick one at local bookstore or online with a good map so you can get acquainted before arriving -

other sites that might help you figure out time/destination are

www.mbta.com
(also has a trip planner, as does hopstop.com, so you can see how long and how to get from point a to b, if you want to walk, take the T , etc...)

Some observations:

1. Springfield is a 2 hour drive or an equivalent bus ride from Boston and not a very attractive city to boot despite about a day's worth of museums to see -- the best I can think to say about Springfield is that it sure beats nearby Holyoke, which is a pit. If you're going out that far, I'd recommend going to Old Sturbridge Village or seeing Northampton/Amherst, which are towns much nicer than Springfield.

2. the JFK Library is well worth a visit, though despite the subway stop name (JFK/UMass), it's actually not an easy walk there from the subway. Allow a little extra time to take the shuttle that runs between the stop and museum, which I'm pretty sure still exists. It may be wise to do this first thing in the day. I'll second the idea of doing the JFK Library in the morning and Harvard Square in the afternoon and evening. Mr. Bartley's is a good place for burgers and fun for the proverbial kids of all ages.

3. Woodman's may be the "historic" place for fried clams, but one can do better food-wise at J.T. Farnham's (also in Essex) or The Clam Box (in Ipswich).

4. Salem is a good option for a day trip, though I agree that (with the exception of the Salem Witch Museum on Washington Square) the "witch based" attractions are best avoided. But there's plenty else, including the Peabody-Essex Museum (especially good), House of Seven Gables, Salem Maritime National Historic Site (including tours of adjacent historic houses), other historic buildings, and a downtown shopping area that's fun to stroll.

5. if you want dim sum in Boston's Chinatown, good places to try are China Pearl, Emperor's (aka Empire) Garden, and Chau Chow City. Hei La Moon is also close by, but supposedly has gone downhill a bit since I tried it (and liked it very much). Imperial Seafood is the weakest of the choices there.

After all the tips and ideas, we have put together a (tentative) itinerary. Here it is (and feel free to add any further ideas or input) I have changed the hotel (AGAIN) to the Westin Boston Waterfront--I know it's a little farther out, but I budgeted for cab money and we don't plan to spend that much time at the hotel, anyway. The rate was just too good to pass up. The itinerary is pretty active, but our boys like to be busy, and we can relax when we get home!

June 29--Arrive Boston, check in at Westin Waterfront; if we get to Boston by early evening, maybe dinner at Legal Seafoods and then the Skywalk at the Prudential Center

June 30
Duck Tour (9 a.m.)
Boston Common,Public Garden, Freedom Trail, lunch/dinner in Faneuil Hall/North End (long day, but we can speed it up or slow it down as desired)

July 1
Fast Ferry to Provincetown
Arts Dune Tours
(Is a whale watch too much to do after a 90-minute ferry ride?)
Spend time on the beach/eat lunch in Provincetown

(Or should we skip this trip entirely and instead do a whale watch out of boston and maybe see Shear Madness in the evening?)



July 2
JFK Museum
Harvard Square (later afternoon and evening with dinner at Mr. Bartley's)

July 3
Day trip to Salem, Portsmouth, Maine, going as far as Ogunquit to walk the Marginal Way. Eat at a lobster shack

If we get back in time, maybe try to catch the Boston Pops rehearsal

July 4
U.S.S. Constitutin harbor cruise
Boston neighborhoods (Back Bay, Beacon Hill, more of the Freedom Trail, etc.)
Fireworks

The only problem I see with your itinerary is trying to fit Salem, Portsmouth, and Ogunquit all in one day -- most especially if you're trying to drive on July 3, when the roads will almost surely be jammed heading out of Boston in all directions. You could in fact easily spend the day in any of these three towns, and I'd personally choose one and let the others go depending on your interests and priorities.

Note that downtown Salem is easily reached by commuter rail from Boston, but takes a while by car as it's not especially close to Route 128 or I-95. And Ogunquit is a good stretch to reach from I-95 as well, as the exit isn't all that close to the town -- and it's extremely impractical (if not utterly impossible) to get to by public transportation. Portsmouth is closest to the interstate highway and can also be reached by bus. So trying to even get to all three towns in a day is well nigh impossible.

Agree with bachslunch, July 3 is a terrible day to try and drive all the places you named- the roads will likely be mobbed -

stay closer and use public transportation - take the ferry to Salem - or train or something - anything but a car -

or some other closer destination or stay local -
if it is a great day do something on Boston Harbor (Georges Island, Spectacle, etc or Charles River)

Look at

www.thetrustees.org

and see if you can find a location you can reach w/out a car or even w a car that is not in such a high traffic route if you want outdoor activitiy

what are you looking for? seaside quaint town? to be on the water? seafood? beach? you are doing PTown, which has that, - I wouldn't venture as far and choose things closer -

Your kids (and you) would love Blue Man Group over Shear Madness. You can get discount tickets at the BosTix kiosks. Get there when they open.

We are back from a great week in Boston. Thanks to everyone for their helpful advice.

We stayed at the Colonnade, which was great, though the service was lacking. We had wonderful meals at La Galleria 33, Pizzeria Regina (best pizza ever), Giacomo's, Legal Seafood (Rowe's Wharf location), Stephanie's on Newbury and Mr. Bartley's. Okay food at Barking Crab and Jasper White's Summer Shack. We got addicted to J.P. Licks and Emack and Bolio ice cream, as well as patries from Mike's and Modern Pastry.

We drove up to Maine one day and spent time walking the Marginal Way, ate at Barnacle Billy's and stopped in Salem on the way back to Boston. The next day, we went to Crane Beach (weather was beautiful). In short, Boston was a great city.