I'd like to cross-post something (with a few clarifications) that I wrote on ArchBoston last night, since I believe it's relevant here.
I've spent some time looking at MassGIS / Oliver, Boston Tax Parcel Viewer, and Lynn and Revere's respective registries of deeds. It appears that the ROW from Revere Street to Point of Pines (minus road crossings) is actually owned by the Massachusetts Electric Company, a National Grid subsidiary, and used as a utility corridor. It is not owned by the state in any fashion; I doubt NG cares too much about enforcing property lines as long as they can access their towers. The utility ROW is mostly about 110 feet wide; the Blue Line ROW is only 30-40 in many locations south of Revere Street. Narrower points of the utility ROW are Revere Street to 354 RB Boulevard (~80 feet due to drainage channel), 354 RBB to Jack Satter House (40 feet), a short section near a couple ponds (47 feet), Mills Avenue jughandle (24 feet), Frank Avenue to Harrington Avenue (40 feet, with a ~2 feet incursion by the 1 Carey Circle Building), Harrington to 1A (29 feet), and past 1A (20 feet). The only real trouble spots for BLX would be the jughandle (reconfigurale), Carey Circle (reconfigure the parking garage access, might have to abandon a few condos which would be literally right next to train wheels), past Harrington (might have to take a few backyard slivers), and the 1A interchange and beyond (would require a BL flyover or a completely rebuilt interchange). There is a substantial amount of wetlands on the 1A side of the ROW; that more than the abutters would complicate reusing it for the Blue Line.
In Lynn, it looks like GE bought up the right of way when they expanded the Riverworks plant during WWII (likely because the BRB&L owned GE a lot for electrification). As far as the Atlantic Toyota property is owned by Lynnway Associates (the Lynnport developers) which bought the GE Gear Plant site in 2014. The 2015 Lynn property map indicates that New England Power Company (another NG subsidiary) has an easement for their power lines. The parcel that Atlantic Toyota's back building and lot sit on (minus the squarish chunk behind Hacienda Corona) were sold to a private developer by GE in 1989. The MBTA acquired from there to Commercial Street in a land swap with GE in 1991. That squarish chunk, plus the wooded area behind Sullivan, were sold to the same private developer in 2014. The final section from Commercial to Market Street has no real current transit value and is owned by various private entities. The Eastern Mass bought the Lynn terminal and a section of the ROW for busway use in January 1941, but by 1968 they'd moved to Central Square (Mt Vernon Street in front of the B&M station) which buses in Lynn used until 2002.
If anyone desires to look them up, parcel numbers are 9-157A-2 in Revere, 035-796-074 (also -082, 083, 084, 092) in Lynn.
In Eastie, Massport owns from Cowper Street to Tomahawk Drive (including a few hundred feet of the Blue Line ROW). A private landowner actually owns the parcels from Tomahawk Drive to just west of Webster Street, including the entire abandoned tunnels. They pay over 5 grand a year in property taxes on undeveloped - and largely undevelopable - land. The former terminal area is owned by the shipyard.
The MBTA owns the Orient Heights yard area. The casket company owns its building (the former BRB&L carhouse). The chunk of land and swamp just east of the MBTA yard is owned by the city via foreclosure, probably after the bankrupt BRB&L declined to pay taxes on property it was unlikely to sell. Most of the Winthrop Loop has been divided up into private property; notable exceptions are the DCR path near Argyle Street, Veterans Road (built on the former ROW), and the former Crystal Cove trestle which is owned by the town.