The 36-year-old head of software giant Lotus Development Corp. eclipsed Chrysler Chairman Lee A. Iacocca last year as the nation's highest-paid boss, according to a list compiled by Business Week.

Lotus Chairman Jim P. Manzi made $26.3 million in salary, bonuses and stock options during 1987, topping the $17.9 million taken home by Iacocca, who had been the top-paid executive of 1986, the magazine said Thursday.Figures were compiled for the annual "Executive Compensation Scoreboard" being published in Business Week's May 2 edition.

The list, which covers 339 companies, shows that with long-term compensation the average chief executive's total pay jumped 48 percent in 1987 to $1.8 million, one of the largest single increases ever.

Business Week attributed the gains largely to stock options that were exercised prior to the Oct. 19 market crash.

Excluding long-term pay, the average chief executive's salary and bonus rose 8 percent to $975,617, much less than the 18 percent average increase in 1986 and slightly below the 8.6 percent that most managers settled for, the magazine said.

The third-highest paid executive was Paul Fireman, chairman of running shoe company Reebok International Ltd., who collected a total of $15.4 million.

Two of the highest-paid bosses worked for the same company, Waste Management Inc. Company President Phillip B. Rooney collected $14.3 million for the No. 4 spot, while Senior Vice President Donald F. Flynn was sixth with $13.2 million.

In a separate analysis of the relationship between pay and company performance over a three-year period, Business Week said the executives who delivered the most to shareholders were Robert A. Swanson, chairman of Genentech, Inc., and Richard G. Cline, chairman of Nicor Inc.

Swanson was credited with giving shareholders of the innovative biotechnology company the largest return in stock appreciation and dividends for the least pay in the past three years. Cline was credited with earning the least relative to the profitability of his company, a natural gas utility.

Business Week said the worst performers were Iacocca and John F. McGillicuddy, head of Manufacturers Hanover Corp.

Iacocca's pay was the highest relative to Chrysler's return to shareholders, while McGillicuddy earned the most measured against the bank's weak financial performance.

Some bosses who lost their jobs were big winners because of so-called "golden parachute" severance awards they had negotiated.

A separate list of the largest severance packages was led by Terrence A. Elkes, ex-chairman of Viacom Inc., who got $25 million after a takeover of his company by National Amusements Inc.