Neil J. Welch, a top candidate last year to become director of the FBI, was named yesterday to take over as head of the New York office, the bureau's largest.

He replaces J. Wallace LaPrade, who was fired last month by Attorney General Griffin B. Bell, for allegedly lying to prosecutors investigating illegal FBI break-ins. LaPrade is appealing the dismissal.

The 51-year-old Welch gained a reputation while special agent in charge of the Buffalo, Detroit and Philadelphia offices over the last 12 years as an innovative executive who maintained some independence from headquarters during the J. Edgar Hoover era.

He also is known as an agent who emphasizes pursuit of political corruption and organized crime, with little interest in surveillance of political dissidents.

Welch was one of five candidates selected as possible successors to FBI Director Clarence Kelley by a presidential commission. Bell bypassed the recommendations and picked U.S. District Court Judge Frank Johnson of Alabama for the post.

An illness forced Johnson to withdraw and Bell then tapped current Director William H. Webster, another federal judge, for the post.

As head of the FBI's Philadelphia office, Welch was in the news earlier this year during the controversy over the Carter administration's firing of Republican U.S. attorney David W. Marston. At the time, Welch urged that Marston be kept on to finish politically sensitive investigations of two Democratic congressmen.

Since Marston's dismissal - he later ran unsuccessfully in the GOP primary for governor - Welch's office has continued probing the allegations that Reps. Daniel J. Flood and Joshua Eilberg profited illegally from construction of a Philadelphia hospital.

As head of the New York office Welch will command more than 800 FBI agents and also hold the title of assistant director, one of the bureau's top dozen positions.