All of those suggestions are good. I'd add emphasis on the Swan Boats (
Swan Boats of Boston ) and the Duck Tours (
Boston Duck Tours - The Official Website & Online Tickets ). If the kids have been to Atlanta's Aquarium, they've experienced one of the best in the nation and may be a bit let down by Boston's. The Museum of Science (
Museum of Science, Boston | Home ) is very interesting and so is the Children's Museum (
Welcome to Boston Children's Museum ).
I'll add a couple more:
The Skywalk Observatory atop Prudential Center:
Skywalk Observatory - The Shops at Prudential Center . It's on the 51st floor of the tower which sits in the middle of a major urban mall so shopping will be good. There's also an observation deck on top of the Custom House Tower that's a bit less traveled:
Marriott's Custom House: For a memorable vacation in Boston
A Red Sox Game could be a heck of an experience.
The Official Site of The Boston Red Sox | redsox.com: Homepage . If you can't get tickets or find that they're too expensive, you can still do a Ball Park Tour which is really cool:
Fenway Park Tours | redsox.com: Ballpark
I would also go walk around Harvard Square and Harvard University. While you're there, you may want to check out Harvard's Museum of Natural History (
Home*-*Harvard Museum of Natural History ). The area is cool, you could easily do lunch and spend an afternoon here.
Take them to the North End and walk around. When you get tired, take a break in Christopher Columbus Park. When you get hungry, grab lunch at one of the little cafes. If the kids have a sweet tooth get some gelato at a local shop or maybe a Cannoli from one of the many bakeries. While you're in the neighborhood, check out Paul Revere's House and the Old North Church. It's cool for all ages.
The Mary Baker Eddy Museum (
The Mary Baker Eddy Library ) may be a bit too grown up for the young guys, but it's VERY interesting. I love the "Mapparium"
Finally, I'd suggest checking out the Museum of Fine Arts (
Museum of Fine Arts, Boston: Home ). I know, I know... 8 and 9 year olds get bored out of their minds looking at art. However, the MFA has a LOT that goes well beyond art that will be fascinating to people of all ages. There are real mummies and actual artifacts from many old cultures that are fascinating regardless of age. I would suggest looking into it.
Some of the best things in Boston are free. I would highly recommend just walking around with everyone and doing a self guided tour. You could visit the Arboretum (
Arnold Arboretum - Visitors ) which is beautiful. I recommend following the Freedom Trail loosely (
The Freedom Trail Foundation and
City of Boston - Freedom Trail ) and turning off the path and stopping at whatever interests you. This will bring you through the North End, Faneuil Hall, the Boston Common (which is worth spending a nice afternoon in), Beacon Hill (absolutely gorgeous) etc. If you choose to go all the way, you can head over to the Bunker Hill Monument (
City of Boston - Bunker Hill Monument ) or Old Iron Sides, aka the U.S.S. Constitution (
Official Web site of USS Constitution "Old Ironsides" ). Boston is constantly rated the most walkable city in the U.S. and walking is the best way to see it.... I would definitely suggest walking and seeing the city as you go. I think your family from Atlanta will appreciate it most this way.
*Edit* I forgot to add: Whale Watching. There are a bunch of different ways to do this. If you're closest to Boston, Boston Harbor Cruises offers a whale watch out of Rowe's Wharf (
http://www.bostonharborcruises.com/boston-whale-watch/ ). If you're on the North Shore, you can catch a boat out of Gloucester:
http://www.7seas-whalewatch.com/ . If you're on the South Shore, you can catch a whale watch boat out of Plymouth:
http://www.captjohn.com/ . There's also Plimoth Plantation and the Mayflower for attractions in Plymouth.
Finally, The BEST way to do a whale watch in New England is to go to Provincetown (
http://www.provincetown.com/ ) on the Cape. I know P-Town is quite a hike, but it ends up being worth it. First, all whale boats (from Gloucester, Boston, Plymouth, P-Town, etc) go to the same spot on the ocean (Stellwagon Bank). It's literally right around the corner from P-Town which is located on the tip of Cape Cod so the boat ride to see whales is FAR shorter than out of any other port... in fact, you can often times see the shore of P-Town while Whale Watching. This alone makes it worth the extra drive (more time whale watching, less time getting to the area to see whales). The Dolphin Fleet is the best group in the business (
http://www.whalewatch.com/dolphinfleet/ ). The other great thing about driving to P-Town is being in P-Town. Shopping and Dining are wonderful in P-Town and so are the beaches. If you do a morning whale watch, you can spend the afternoon on the beaches and evening shopping. I'd also visit and climb the Pilgrim Monument (aka P-Town Tower):
http://www.pilgrim-monument.org/t3/index.php . This is worth a day and it'll be a wonderful way to show the family what quintessential New England is.