Changes include removing traffic islands and extending sidewalks at Fulton Street and Utica Avenue.
The route will free up lanes for buses that travel on Cross Bay and Woodhaven boulevards.
The city plans to install Select Bus Service on East 86th Street by the spring.
Trips to LaGuardia Airport from West 106th Street are about 10 minutes faster.
The MTA is hoping to decrease delays along the West 86th Street route with faster service.
Buses on the M60 line are clogging Broadway and creating a safety hazard, residents said.
Politicians lauded the new service, but advocates for the disabled said more could be done to help them.
Select Bus Service on the M60 LaGuardia Airport bus is slated to begin May 25.
The long winter pushed back the debut of the controversial service on the M60 bus line.
The $17.5 million construction project has been underway for more than two years.
The new plan will add a stop at Gates Avenue on both Nostrand Avenue and Bedford Avenue.
Merchants and drivers say the traffic shift has caused major problems on Nostrand Avenue.
The express bus line serves Williamsburg, Bed-Stuy, Crown Heights, Flatbush, Midwood and Sheepshead Bay.
Adriano Espaillat and Melissa Mark-Viverito want to revive the plan to speed bus service in Harlem.
The agencies said they were not able to resolve conflicts with the local community over the plan.
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