Beacon Park and the old Sears and Coke warehouse sites across Cambridge St are about 200 acres altogether, and Harvard is probably not doing anything with them soon. An olympic village there would see immediate reuse as student housing, and BU has already set a trend for highrises along the Charles.
Harvard Stadium is also RIGHT THERE and could have the northern seats added back, as well as some nosebleads attached to the existing structure that could be removed after the event.
Nickerson Field could probably also be converted back into its Braves Field capacity (or greater) since its surrounded by a decent amount of green space, even after the towers were build around it. Hell, you could probably demolish everything bounded by Gardner, Malvern, Babcock and Beacon Park for a large stadium too.
Those two facilities could hold some of the lower-key events, then you really just have to build one main stadium, which seems like a good fit somewhere in the South Bay.
Edit: I gave this a bit more thought afterwards:
I didn't worry about any of the facilities in London with capacity's under 10,000 as they are abundant at our surrounding colleges.
Gymnastics/Basketball Finals:
TD Garden
(18,624 Celtics, 20,000 London)
Field Hockey:
Nickerson (nee Braves) Field
(10,000 as Nickerson, 40,000 as Braves, 16,000 London)
Boxing, Fencing, Judo, Table Tennis, Taekwondo, Weightlifting, Wrestling:
BCEC + Hynes
(basically the same as the ExCeL)
Modern Pentathlon (running, shooting):
Franklin Park
(527 acres Boston, 180 acres London)
---you could probably do it in Allston too as there are a ton of parks along the Charles---
Equestrian:
Suffolk Downs
Tennis:
Harvard Stadium
(30,323 current, 57,166 old, 30,000 London)
---I would really like to see Harvard Stadium used no matter what, since it's design is based off the stadium from the first modern olympics---
Outdoor Vollyball:
Moakley Park, Southie
(comparable in size to London's venue)
Indoor Volleyball:
??? Maybe a temp structure over Steinbrenner Stadium?
(15,000 London)
Diving, Modern Pentathlon (swimming), Swimming, Synchronized Swimming:
New Permenant structure at the abandoned piers south of Maverick Square
(260'x520' London, 440'x600'Eastie)
All the boating events would take place on the Charles, but you could use Pleasure Bay for some things too as it is free of waves, and perhaps even the Chestnut Hill Reservoir.
Olympic Stadium / Soccer Finals:
New Permanant Venue, reducable in size.
(90,000 London)