The savings and loan industry is awash in a sea of red ink, but chief executives of the largest thrifts are doing quite well - earning an average of $250,000 a year, according to a study released Tuesday.

The 1988 Real Estate Executive Compensation review issued by Ferguson Partners Ltd. said that, while thrifts posted a record $12.1 billion loss last year, the losses were not reflected in executives paychecks."The CEOs of thrift institutions of $5.1 billion plus in assets are as well compensated as their counterparts in residential mortgage banks," said William J. Ferguson, managing partner of the consulting firm.

Both earned an average of $250,000 a year plus bonuses averaging 50 percent to 100 percent of their base salaries.

But lower ranking senior executives did better at commercial banks than at S&Ls.

Real estate department heads at major commercial banks earned salaries between $175,000 and $200,000 with bonuses of 50 to 100 percent, while counterparts at major thrifts earned $125,000 to $150,000, plus bonuses of 50 to 100 percent.

Commercial workout department heads at commercial banks earn salaries of $150,000 plus bonuses of 50 to 100 percent, while S&L commercial workout heads earn an average base salary of $100,000 to $150,000 and 50 percent bonuses.

The survey reviewed salaries at 500 residential mortgage banks, thrifts, insurance companies, real estate development firms, full service real estate firms, commercial mortgage bankers, pension fund advisers, major investment banks, major real estate consulting firms, architectural firms and corporations.