AFP reports citing local media.
One police officer was shot dead and a second wounded in the dramatic nighttime operation, authorities said.
One suspect was caught in Watertown near Boston after a chase in which explosives and gunfire were heard, the Boston Globe reported.
Special police forces sealed off much of the town as they hunted the second man, the newspaper and other media said.
The authorities made no comment on whether there was a link between the manhunt and Monday's bombing in which three people were killed and about 180 injured.
But the operation came only hours after the Federal Bureau of Investigation released photos of the suspects they believe planted the bombs.
A robbery at a gas station was followed by the killing of a police officer on the campus of Massachusetts Institute of Technology and a car chase to Watertown, media reports said.
A second police officer was wounded in a gunfight in the town, they added.