Since you only have a weekend you wont really be able to appreciate the full boston as you really need a week to explore everything
I would suggest...
1.) Taking the train in early - from your hotel -
SAMPLE ITENERARY
SAT -
Start early -
have breakfast at hotel
take commuter rail in or subway in
The Blue Line - AQUARIUM STOP at the waterfront -
take the waterfront exit/aquarium exit and go to the trolley tour booth -
take an OLD TOWN TROLLEY TOUR which gives you a goiod overview of the city, (Do the full circuit loop)
When you're done - consider taking a Harbor cruise of the harbor from Boston Harbor Cruises.
After that have lunch at Legal Seafoods - or the Cafe near the Boston Harbor cruises.
Next do the freedom trail the rest of the afternoon -
Start at Park st (RED or Green Line) Boston Common
walk the freedom trail . - see the old north church, copp's hill burial ground, old south meeting house, King's chapel, Paul Revere's house -
and the Constitution ship and museum - Charlestown Navy Yard
Climb up the Bunker Hill monument
check out the battleship USS Cassin Young (all on the freedom trail)
Don't miss the presentation (The "Whites of their eyes" Pavillion")
Have Dinner in the North End at one of the Italian Restaurants on your way back
Take the Inner Harbor Ferry back from Charlestown Navy Yard pier to Long Wharf by the Aquarium
Inner Harbor Ferry - Charlestown - Boston, MA
Walk through Quincy Market on your way back and head on over to the Fours Bar by North Station, or one of the other bars near the Boston Garden for a beer and a dinner, before heading home -
if you have time you might consider going up the Prudential Tower - at Night to check out the night view. and contrst it with the day view you'll get at Brunch tomorrow at the top of the hub restaurant :-)
SUNDAY
Make a reservation in advance for the TOP Of the HUB's sunday brunch
you get a sweeping panoramic view of Boston (11:30 am start so be there by 11am)- COpley pLace. - at the Prudential tower -
Top of the Hub
Make your reservation online and enjoy the brunch and view of Boston
then you'll be near the Copley place mall, so take a stroll through the shops and such - and then
Go to the Public Gardens to check out the tulips and take a ride on the Swan Boats and see the Make Way for Ducklings Island and statue, from there, walk down commonwealth ave and check out the old brownstones and the beautiful statues and trees. take comm ave. to kenmore square and (See if they are having tours that day of the Ballpark
INDIVIDUAL RATES
Adults ... $12
Seniors ... $11
Children (3-15) ... $10
ACCESSIBILITY
Tours are fully handicap accessible. Please contact the tour office at 617-226-6666 for additional assistance.
HOURS OF OPERATION
9 a.m. - 4 p.m., every hour on the hour, or until 3 hours prior to game time
VISIT INCLUDES
50 minute walking tour of the ballpark, guided by an official Fenway Park Tour Guide. All areas are subject to availability.
Have lunch at the Bleacher Bar - which has a view of the field from some of the tables.
On the way back go back up Newbury St. in the evening - and afternoon and check out the shops, - and such maybe an ice cream cone at J P Licks -
make your way through the public gardens and make your way over to the Bull and Finch Pub to check out the front of cheers and take your picture under the sign (Dont bother going in this isn't the real cheers) walk across the common to Downtown Crossings/State Street, and make your way through Government Center to Quincy market, check out the street performers, shops, etc. and maybe eat at one of the Irish pubs along state street (the Black Rose, Kitty O'shea's etc.) ,
From Quincy Market you can walk to North Station - or catch the "T" a couple stops
to get the commuter rail back. or take the subway back
Definitely check out the Duck Tours
Boston Duck Tours - The Official Website & Online Tickets
A harbor tour
Boston Harbor Cruises, Whale Watch, Provincetown Ferry, Boston Sightseeing Tours
Dinner at the North End
The North End - Boston's Little Italy
Freedom Trail
The Freedom Trail Foundation
Museum of Science and Omni theater
Museum of Science, Boston | Home
Prudential Skywalk Observatory
Skywalk Observatory - The Shops at Prudential Center
Copley place mall
Simon Malls | More Choices — Copley Place Information, Copley Place Gift Cards
Old Town Trolley Tour Boston
Boston Tours | Boston Attractions | Old Town Trolley Tours® covering Beacon Hill, Fenway Park, Boston Tea Party, New England Aquarium
Fenway PArk tour
Fenway Park Tours | redsox.com: Ballpark
Dinner Fours Bar:
The Four's - Restaurant & Sports Bar
Lunch - Bleacher Bar
Bleacher Bar - Fenway - Boston, MA
Bleacher Bar
New England Aquarium
New England Aquarium Home
Museum of Fine arts
Museum of Fine Arts, Boston: Home
Boston Harbor walk
The Boston Harborwalk
Boston Irish Pubs
Boston Irish Pubs