Have you check the Google Map Tour Guide Central? There are a lot of great suggestions for NYC and Boston from the Archinect netizens.

Office DA's Macallen building in South Boston is worth checking out and I don't believe its on the Tour Guide Central entry for B-town.

MOMA, American Folk Art Museum, AMNH Rose Center for Earth and Space, Hearst Tower, or Paul Rudolph's Loft

the new museum just opened...on Bowery and spring

Boston: 33 Arch St., Boston Intercontinental Hotel, Manulife Building, Independence Wharf

Boston:
Personally I think the intercontinental hotel, independence wharf are really bland corporate architecture you can see anywhere (though that would definitely be representative of boston architecture at large)

For recent work and practicing architects:
Macallen Building (office dA) - Red Line / Broadway Station
ICA (Diller scofidio) - Silver/Courthouse
Allston Library (Machado Silvetti) - 66 or 86 bus from Harvard Sq
One Western Ave (Machado Silvetti) - Red/Central and a healthy walk or 70A Bus
Wellesley Student Ctr (Scoggin Elam) - Commuter Rail to Wellesley Sq or car
Simmons Hall (Holl) - Red/Kendall MIT
Stata Center (Gehry) - Red/Kendall MIT
Newbury Street Renovation (Gehry) - Green/Hynes
Genzyme (Behnisch) - Red/Kendall

There are some interesting things under construction right now by Moneo, Kyu Sung Woo, office DA, architectsAlliance, Stephen Erlich, Foster, Piano, and an Apple store glass box, so if you're not coming til later in the year do some googling

mid-late 20th Century:
City Hall (Kallman McKinnell Wood) - Green or Blue/Govt Ctr
JFK Bldg (TAC) - Green or Blue/Govt Ctr
Blue Cross Bldg (Rudolph) - Red/South Station
State Services Building (Rudolph) - Blue/Bowdoin or Red/Charles
Federal Reserve Bank (Stubbins) - Red/South Station
North End Library (Carl Koch) - Green/Haymarket
Carpenter Center (Corbusier) - Red/Harvard
Graduate Center (Gropius) - Red/Harvard
Gund Hall (John Andrews) - Red/Harvard
Peabody Terrace (Sert) - Red/Central or Harvard and a walk
American Rep Theater (Hugh Stubbins) - Red/Harvard
MIT Chapel (Saarinen) - Red/Kendall
Kresge Auditorium (Saarinen) - Red/Kendall
Baker Hall (Aalto) - Red/Kendall

If you have access to a car, definitely go to concord to tour the Gropius House (30 minute drive), and if you go around the corner and do some trespassing/sneaking you can see one of Breuer's houses.

If you're a Pei/Cobb fan add an extra day to your trip, but if not there isn't anything really worth seeing save for the Christian Science Center (Green-D/Symphony). The Hancock tower is a masterpiece but the experience you get of it moving around the city is where its at, there is no interaction with it on its site.

Early 20th century and historic, in approximate reverse chronology:

Boston Library (McKim Mead White) - Green/Copley
Trinity Church (Richardson) - Green/Copley
Stoughton House (Richardson) - Red/Harvard
New Statehouse (Bulfinch) - Red/Park
St. Stephen's Church (Bulfinch) - Green/Haymarket or Blue/Aquarium
Paul Revere House - Green/Haymarket or Blue/Aquarium

Again, if you're a Richardson fan it is worth renting a car and spending a day visiting the region. He has some fantastic work spanning his whole career here, and much of it is well maintained and open to the public. Many accompany Olmsted landscapes as well.

If you're a historian Boston has a nice collection of 19th century townhouses and urban vernacular. Any book by Bainbridge Bunting is a good guide.

If you have questions feel free to email me.

that's a good list randscraper;

I'd add the Batterymarch Hotel (on Batterymarch street, though it fronts on Broad street too). One of the first art deco buildings in Boston and has 33 colors of brick on the facade, ranging from reddish at the bottom to yellowish at the top, kind of like it's on fire.